Publications – ABC Group

2023

N. Hashemi, B. Hao, M. Ignatov, I. C. Paschalidis, P. Vakili, S. Vajda, and D. Kozakov, “Improved prediction of mhc-peptide binding using protein language models,” Frontiers in bioinformatics, vol. 3, 2023.
[BibTeX]

@article{hashemi2023improved,
Author = {Hashemi, Nasser and Hao, Boran and Ignatov, Mikhail and Paschalidis, Ioannis Ch and Vakili, Pirooz and Vajda, Sandor and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Frontiers in Bioinformatics},
Publisher = {Frontiers Media SA},
Title = {Improved prediction of MHC-peptide binding using protein language models},
Volume = {3},
Year = {2023}}

I. T. Desta, S. Kotelnikov, G. Jones, U. Ghani, M. Abyzov, Y. Kholodov, D. M. Standley, M. Sabitova, D. Beglov, S. Vajda, and others, “Mapping of antibody epitopes based on docking and homology modeling,” Proteins: structure, function, and bioinformatics, vol. 91, iss. 2, p. 171–182, 2023.
[BibTeX]

@article{desta2023mapping,
Author = {Desta, Israel T and Kotelnikov, Sergei and Jones, George and Ghani, Usman and Abyzov, Mikhail and Kholodov, Yaroslav and Standley, Daron M and Sabitova, Maria and Beglov, Dmitri and Vajda, Sandor and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {2},
Pages = {171--182},
Publisher = {John Wiley \& Sons, Inc. Hoboken, USA},
Title = {Mapping of antibody epitopes based on docking and homology modeling},
Volume = {91},
Year = {2023}}

S. Chen, M. Hassan, R. L. Jernigan, K. Jia, D. Kihara, A. Kloczkowski, S. Kotelnikov, D. Kozakov, J. Liang, A. Liwo, and others, “Protein folds vs. protein folding: differing questions, different challenges,” Proceedings of the national academy of sciences, vol. 120, iss. 1, p. e2214423119, 2023.
[BibTeX]

@article{chen2023protein,
Author = {Chen, Shi-Jie and Hassan, Mubashir and Jernigan, Robert L and Jia, Kejue and Kihara, Daisuke and Kloczkowski, Andrzej and Kotelnikov, Sergei and Kozakov, Dima and Liang, Jie and Liwo, Adam and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Proceedings of the National Academy of Sciences},
Number = {1},
Pages = {e2214423119},
Publisher = {National Academy of Sciences},
Title = {Protein folds vs. protein folding: Differing questions, different challenges},
Volume = {120},
Year = {2023}}

S. J. Wodak, S. Vajda, M. F. Lensink, D. Kozakov, and P. A. Bates, “Critical assessment of methods for predicting the 3d structure of proteins and protein complexes,” Annual review of biophysics, vol. 52, p. 183–206, 2023.
[BibTeX]

@article{wodak2023critical,
Author = {Wodak, Shoshana J and Vajda, Sandor and Lensink, Marc F and Kozakov, Dima and Bates, Paul A},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Annual Review of Biophysics},
Pages = {183--206},
Publisher = {Annual Reviews},
Title = {Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes},
Volume = {52},
Year = {2023}}

I. Paul, D. Bolzan, A. Youssef, K. A. Gagnon, H. Hook, G. Karemore, M. U. Oliphant, W. Lin, Q. Liu, S. Phanse, and others, “Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in emt,” Nature communications, vol. 14, iss. 1, p. 688, 2023.
[BibTeX]

@article{paul2023parallelized,
Author = {Paul, Indranil and Bolzan, Dante and Youssef, Ahmed and Gagnon, Keith A and Hook, Heather and Karemore, Gopal and Oliphant, Michael UJ and Lin, Weiwei and Liu, Qian and Phanse, Sadhna and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Nature communications},
Number = {1},
Pages = {688},
Publisher = {Nature Publishing Group UK London},
Title = {Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT},
Volume = {14},
Year = {2023}}

M. Ignatov, A. Jindal, S. Kotelnikov, D. Beglov, G. Posternak, X. Tang, P. Maisonneuve, G. Poda, R. A. Batey, F. Sicheri, and others, “High accuracy prediction of protac complex structures,” Journal of the american chemical society, vol. 145, iss. 13, p. 7123–7135, 2023.
[BibTeX]

@article{ignatov2023high,
Author = {Ignatov, Mikhail and Jindal, Akhil and Kotelnikov, Sergei and Beglov, Dmitri and Posternak, Ganna and Tang, Xiaojing and Maisonneuve, Pierre and Poda, Gennady and Batey, Robert A and Sicheri, Frank and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of the American Chemical Society},
Number = {13},
Pages = {7123--7135},
Publisher = {American Chemical Society},
Title = {High Accuracy Prediction of PROTAC Complex Structures},
Volume = {145},
Year = {2023}}

I. T. Desta, S. Kotelnikov, G. Jones, U. Ghani, M. Abyzov, Y. Kholodov, D. M. Standley, D. Beglov, S. Vajda, and D. Kozakov, “The cluspro abemap web server for the prediction of antibody epitopes,” Nature protocols, p. 1–27, 2023.
[BibTeX]

@article{desta2023cluspro,
Author = {Desta, Israel T and Kotelnikov, Sergei and Jones, George and Ghani, Usman and Abyzov, Mikhail and Kholodov, Yaroslav and Standley, Daron M and Beglov, Dmitri and Vajda, Sandor and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Nature Protocols},
Pages = {1--27},
Publisher = {Nature Publishing Group UK London},
Title = {The ClusPro AbEMap web server for the prediction of antibody epitopes},
Year = {2023}}

M. Lensink, G. Brysbaert, N. Raouraoua, P. Bates, M. Giulini, R. V. Honorato, C. van Noort, J. Teixeira, A. M. Bonvin, R. Kong, and others, “Impact of alphafold on structure prediction of protein complexes: the casp15-capri experiment,” Authorea preprints, 2023.
[BibTeX]

@article{lensink2023impact,
Author = {Lensink, Marc and Brysbaert, Guillaume and Raouraoua, Nessim and Bates, Paul and Giulini, Marco and Honorato, Rodrigo Vargas and van Noort, Charlotte and Teixeira, Jo{\~a}o and Bonvin, Alexandre MJJ and Kong, Ren and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Authorea Preprints},
Publisher = {Authorea},
Title = {Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment},
Year = {2023}}

S. Kotelnikov, R. Ashizawa, K. I. Popov, O. Khan, M. Ignatov, S. X. Li, M. Hassan, E. A. Coutsias, G. Poda, D. Padhorny, and others, “Accurate ligand–protein docking in casp15 using the cluspro ligtbm server,” Proteins: structure, function, and bioinformatics, 2023.
[BibTeX]

@article{kotelnikov2023accurate,
Author = {Kotelnikov, Sergei and Ashizawa, Ryota and Popov, Konstantin I and Khan, Omeir and Ignatov, Mikhail and Li, Stan Xiaogang and Hassan, Mosavverul and Coutsias, Evangelos A and Poda, Gennady and Padhorny, Dzmitry and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Publisher = {John Wiley \& Sons, Inc. Hoboken, USA},
Title = {Accurate ligand--protein docking in CASP15 using the ClusPro LigTBM server},
Year = {2023}}

2022

T. Nguyen, K. L. Phan, D. Kozakov, S. B. Gabelli, D. F. Kreitler, L. C. Andrews, J. Jakoncic, R. M. Sweet, A. S. Soares, and H. J. Bernstein, “A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs,” Acta crystallographica section d: structural biology, vol. 78, iss. 3, p. 268–277, 2022.
[BibTeX]

@article{nguyen2022simple,
Author = {Nguyen, Thu and Phan, Kim L and Kozakov, Dima and Gabelli, Sandra B and Kreitler, Dale F and Andrews, Lawrence C and Jakoncic, Jean and Sweet, Robert M and Soares, Alexei S and Bernstein, Herbert J},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Acta Crystallographica Section D: Structural Biology},
Number = {3},
Pages = {268--277},
Publisher = {International Union of Crystallography},
Title = {A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs},
Volume = {78},
Year = {2022}}

A. Davila, Z. Xu, S. Li, J. Rozewicki, J. Wilamowski, S. Kotelnikov, D. Kozakov, S. Teraguchi, and D. M. Standley, “Abadapt: an adaptive approach to predicting antibody–antigen complex structures from sequence,” Bioinformatics advances, vol. 2, iss. 1, p. vbac015, 2022.
[BibTeX]

@article{davila2022abadapt,
Author = {Davila, Ana and Xu, Zichang and Li, Songling and Rozewicki, John and Wilamowski, Jan and Kotelnikov, Sergei and Kozakov, Dima and Teraguchi, Shunsuke and Standley, Daron M},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Bioinformatics Advances},
Number = {1},
Pages = {vbac015},
Publisher = {Oxford University Press},
Title = {AbAdapt: an adaptive approach to predicting antibody--antigen complex structures from sequence},
Volume = {2},
Year = {2022}}

M. Egbert, G. Jones, M. R. Collins, D. Kozakov, and S. Vajda, “Ftmove: a web server for detection and analysis of cryptic and allosteric binding sites by mapping multiple protein structures,” Journal of molecular biology, vol. 434, iss. 11, p. 167587, 2022.
[BibTeX]

@article{egbert2022ftmove,
Author = {Egbert, Megan and Jones, George and Collins, Matthew R and Kozakov, Dima and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of molecular biology},
Number = {11},
Pages = {167587},
Publisher = {Academic Press},
Title = {FTMove: A web server for detection and analysis of cryptic and allosteric binding sites by mapping multiple protein structures},
Volume = {434},
Year = {2022}}

G. Jones, A. Jindal, U. Ghani, S. Kotelnikov, M. Egbert, N. Hashemi, S. Vajda, D. Padhorny, and D. Kozakov, “Elucidation of protein function using computational docking and hotspot analysis by cluspro and ftmap,” Acta crystallographica section d: structural biology, vol. 78, iss. 6, p. 690–697, 2022.
[BibTeX]

@article{jones2022elucidation,
Author = {Jones, George and Jindal, Akhil and Ghani, Usman and Kotelnikov, Sergei and Egbert, Megan and Hashemi, Nasser and Vajda, Sandor and Padhorny, Dzmitry and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Acta Crystallographica Section D: Structural Biology},
Number = {6},
Pages = {690--697},
Publisher = {International Union of Crystallography},
Title = {Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap},
Volume = {78},
Year = {2022}}

A. E. Wakefield, D. Kozakov, and S. Vajda, “Mapping the binding sites of challenging drug targets,” Current opinion in structural biology, vol. 75, p. 102396, 2022.
[BibTeX]

@article{wakefield2022mapping,
Author = {Wakefield, Amanda E and Kozakov, Dima and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Current opinion in structural biology},
Pages = {102396},
Publisher = {Elsevier Current Trends},
Title = {Mapping the binding sites of challenging drug targets},
Volume = {75},
Year = {2022}}

G. Jones, A. E. Wakefield, J. Triplett, K. Idrissa, J. Goebel, D. Kozakov, and S. Vajda, “Api development increases access to shared computing resources at boston university,” Journal of software engineering and applications, vol. 15, iss. 6, p. 197, 2022.
[BibTeX]

@article{jones2022api,
Author = {Jones, George and Wakefield, Amanda E and Triplett, Jeff and Idrissa, Kojo and Goebel, James and Kozakov, Dima and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of software engineering and applications},
Number = {6},
Pages = {197},
Publisher = {NIH Public Access},
Title = {API Development Increases Access to Shared Computing Resources at Boston University},
Volume = {15},
Year = {2022}}

P. C. Havugimana, R. K. Goel, S. Phanse, A. Youssef, D. Padhorny, S. Kotelnikov, D. Kozakov, and A. Emili, “Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery,” Nature communications, vol. 13, iss. 1, p. 4043, 2022.
[BibTeX]

@article{havugimana2022scalable,
Author = {Havugimana, Pierre C and Goel, Raghuveera Kumar and Phanse, Sadhna and Youssef, Ahmed and Padhorny, Dzmitry and Kotelnikov, Sergei and Kozakov, Dima and Emili, Andrew},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Nature communications},
Number = {1},
Pages = {4043},
Publisher = {Nature Publishing Group UK London},
Title = {Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery},
Volume = {13},
Year = {2022}}

Q. Zhang, C. S. Kounde, M. Mondal, J. L. Greenfield, J. R. Baker, S. Kotelnikov, M. Ignatov, C. P. Tinworth, L. Zhang, D. Conole, and others, “Light-mediated multi-target protein degradation using arylazopyrazole photoswitchable protacs (ap-protacs),” Chemical communications, vol. 58, iss. 78, p. 10933–10936, 2022.
[BibTeX]

@article{zhang2022light,
Author = {Zhang, Qisi and Kounde, Cyrille S and Mondal, Milon and Greenfield, Jake L and Baker, Jennifer R and Kotelnikov, Sergei and Ignatov, Mikhail and Tinworth, Christopher P and Zhang, Leran and Conole, Daniel and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Chemical Communications},
Number = {78},
Pages = {10933--10936},
Publisher = {Royal Society of Chemistry},
Title = {Light-mediated multi-target protein degradation using arylazopyrazole photoswitchable PROTACs (AP-PROTACs)},
Volume = {58},
Year = {2022}}

A. E. Wakefield, D. Bajusz, D. Kozakov, G. M. Keser{H u}, and S. Vajda, “Conservation of allosteric ligand binding sites in g-protein coupled receptors,” Journal of chemical information and modeling, vol. 62, iss. 20, p. 4937–4954, 2022.
[BibTeX]

@article{wakefield2022conservation,
Author = {Wakefield, Amanda E and Bajusz, D{\'a}vid and Kozakov, Dima and Keser{\H u}, Gy{\"o}rgy M and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of Chemical Information and Modeling},
Number = {20},
Pages = {4937--4954},
Publisher = {American Chemical Society},
Title = {Conservation of allosteric ligand binding sites in G-Protein coupled receptors},
Volume = {62},
Year = {2022}}

2021

S. Vajda, K. A. Porter, and D. Kozakov, “Progress toward improved understanding of antibody maturation,” Current opinion in structural biology, vol. 67, p. 226–231, 2021.
[BibTeX]

@article{vajda2021progress,
Author = {Vajda, Sandor and Porter, Kathryn A and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Current opinion in structural biology},
Pages = {226--231},
Publisher = {Elsevier Current Trends},
Title = {Progress toward improved understanding of antibody maturation},
Volume = {67},
Year = {2021}}

S. Sotudian, I. T. Desta, N. Hashemi, S. Zarbafian, D. Kozakov, P. Vakili, S. Vajda, and I. C. Paschalidis, “Improved cluster ranking in protein–protein docking using a regression approach,” Computational and structural biotechnology journal, vol. 19, p. 2269–2278, 2021.
[BibTeX]

@article{sotudian2021improved,
Author = {Sotudian, Shahabeddin and Desta, Israel T and Hashemi, Nasser and Zarbafian, Shahrooz and Kozakov, Dima and Vakili, Pirooz and Vajda, Sandor and Paschalidis, Ioannis Ch},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Computational and structural biotechnology journal},
Pages = {2269--2278},
Publisher = {Elsevier},
Title = {Improved cluster ranking in protein--protein docking using a regression approach},
Volume = {19},
Year = {2021}}

M. Egbert, K. A. Porter, U. Ghani, S. Kotelnikov, T. Nguyen, R. Ashizawa, D. Kozakov, and S. Vajda, “Conservation of binding properties in protein models,” Computational and structural biotechnology journal, vol. 19, p. 2549–2566, 2021.
[BibTeX]

@article{egbert2021conservation,
Author = {Egbert, Megan and Porter, Kathryn A and Ghani, Usman and Kotelnikov, Sergei and Nguyen, Thu and Ashizawa, Ryota and Kozakov, Dima and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Computational and structural biotechnology journal},
Pages = {2549--2566},
Publisher = {Elsevier},
Title = {Conservation of binding properties in protein models},
Volume = {19},
Year = {2021}}

I. Paul, D. Bolzan, A. Youssef, K. A. Gagnon, H. Hook, G. Karemore, M. U. Oliphant, W. Lin, Q. Liu, S. Phanse, and others, “A multi-tiered map of emt defines major transition points and identifies vulnerabilities,” Biorxiv, p. 2021–06, 2021.
[BibTeX]

@article{paul2021multi,
Author = {Paul, Indranil and Bolzan, Dante and Youssef, Ahmed and Gagnon, Keith A and Hook, Heather and Karemore, Gopal and Oliphant, Michael UJ and Lin, Weiwei and Liu, Qian and Phanse, Sadhna and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {bioRxiv},
Pages = {2021--06},
Publisher = {Cold Spring Harbor Laboratory},
Title = {A multi-tiered map of EMT defines major transition points and identifies vulnerabilities},
Year = {2021}}

R. M. Hekman, A. J. Hume, R. K. Goel, K. M. Abo, J. Huang, B. C. Blum, R. B. Werder, E. L. Suder, I. Paul, S. Phanse, and others, “Actionable cytopathogenic host responses of human alveolar type 2 cells to sars-cov-2,” Molecular cell, vol. 81, iss. 1, p. 212, 2021.
[BibTeX]

@article{hekman2021actionable,
Author = {Hekman, Ryan M and Hume, Adam J and Goel, Raghuveera Kumar and Abo, Kristine M and Huang, Jessie and Blum, Benjamin C and Werder, Rhiannon B and Suder, Ellen L and Paul, Indranil and Phanse, Sadhna and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Molecular cell},
Number = {1},
Pages = {212},
Publisher = {Elsevier},
Title = {Actionable cytopathogenic host responses of human alveolar type 2 cells to SARS-CoV-2},
Volume = {81},
Year = {2021}}

E. N. Muratov, R. Amaro, C. H. Andrade, N. Brown, S. Ekins, D. Fourches, O. Isayev, D. Kozakov, J. L. Medina-Franco, K. M. Merz, and others, “A critical overview of computational approaches employed for covid-19 drug discovery,” Chemical society reviews, vol. 50, iss. 16, p. 9121–9151, 2021.
[BibTeX]

@article{muratov2021critical,
Author = {Muratov, Eugene N and Amaro, Rommie and Andrade, Carolina H and Brown, Nathan and Ekins, Sean and Fourches, Denis and Isayev, Olexandr and Kozakov, Dima and Medina-Franco, Jos{\'e} L and Merz, Kenneth M and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Chemical Society Reviews},
Number = {16},
Pages = {9121--9151},
Publisher = {Royal Society of Chemistry},
Title = {A critical overview of computational approaches employed for COVID-19 drug discovery},
Volume = {50},
Year = {2021}}

M. Egbert, U. Ghani, R. Ashizawa, S. Kotelnikov, T. Nguyen, I. Desta, N. Hashemi, D. Padhorny, D. Kozakov, and S. Vajda, “Assessing the binding properties of casp14 targets and models,” Proteins: structure, function, and bioinformatics, vol. 89, iss. 12, p. 1922–1939, 2021.
[BibTeX]

@article{egbert2021assessing,
Author = {Egbert, Megan and Ghani, Usman and Ashizawa, Ryota and Kotelnikov, Sergei and Nguyen, Thu and Desta, Israel and Hashemi, Nasser and Padhorny, Dzmitry and Kozakov, Dima and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {12},
Pages = {1922--1939},
Publisher = {John Wiley \& Sons, Inc. Hoboken, USA},
Title = {Assessing the binding properties of CASP14 targets and models},
Volume = {89},
Year = {2021}}

M. F. Lensink, G. Brysbaert, T. Mauri, N. Nadzirin, S. Velankar, R. A. Chaleil, T. Clarence, P. A. Bates, R. Kong, B. Liu, and others, “Prediction of protein assemblies, the next frontier: the casp14-capri experiment,” Proteins: structure, function, and bioinformatics, vol. 89, iss. 12, p. 1800–1823, 2021.
[BibTeX]

@article{lensink2021prediction,
Author = {Lensink, Marc F and Brysbaert, Guillaume and Mauri, Th{\'e}o and Nadzirin, Nurul and Velankar, Sameer and Chaleil, Raphael AG and Clarence, Tereza and Bates, Paul A and Kong, Ren and Liu, Bin and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {12},
Pages = {1800--1823},
Publisher = {John Wiley \& Sons, Inc. Hoboken, USA},
Title = {Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment},
Volume = {89},
Year = {2021}}

U. Ghani, I. Desta, A. Jindal, O. Khan, G. Jones, N. Hashemi, S. Kotelnikov, D. Padhorny, S. Vajda, and D. Kozakov, “Improved docking of protein models by a combination of alphafold2 and cluspro,” Biorxiv, p. 2021–09, 2021.
[BibTeX]

@article{ghani2021improved,
Author = {Ghani, Usman and Desta, Israel and Jindal, Akhil and Khan, Omeir and Jones, George and Hashemi, Nasser and Kotelnikov, Sergey and Padhorny, Dzmitry and Vajda, Sandor and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Biorxiv},
Pages = {2021--09},
Publisher = {Cold Spring Harbor Laboratory},
Title = {Improved docking of protein models by a combination of alphafold2 and cluspro},
Year = {2021}}

L. C. L. Andrews, J. Jakoncic, R. Sweet, H. Bernstein, and D. Kozakov, “Probing drug-protein interactions with microed,” Foundations of crystallography, vol. 77, p. a265, 2021.
[BibTeX]

@article{andrews2021probing,
Author = {Andrews, Lisa Clark1 Larry and Jakoncic, Jean and Sweet, Robert and Bernstein, Herbert and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Foundations of Crystallography},
Pages = {a265},
Title = {Probing drug-protein interactions with MicroED},
Volume = {77},
Year = {2021}}

A. Jindal, S. Kotelnikov, D. Padhorny, D. Kozakov, Y. Zhu, R. Chowdhury, and S. Vajda, “Side-chain packing using se (3)-transformer,” in Pacific symposium on biocomputing 2022, 2021, p. 46–55.
[BibTeX]

@inproceedings{jindal2021side,
Author = {Jindal, Akhil and Kotelnikov, Sergei and Padhorny, Dzmitry and Kozakov, Dima and Zhu, Yimin and Chowdhury, Rezaul and Vajda, Sandor},
Booktitle = {PACIFIC SYMPOSIUM ON BIOCOMPUTING 2022},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Pages = {46--55},
Title = {Side-chain packing using se (3)-transformer},
Year = {2021}}

T. Nguyen, K. L. Phan, D. Kozakov, S. B. Gabelli, D. F. Kreitler, L. C. Andrews, J. Jakoncic, R. M. Sweet, A. S. Soares, and H. J. Bernstein, “A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs,” in Acta crystallographica a-foundation and advances, 2021, p. C771–C771.
[BibTeX]

@inproceedings{nguyen2021simple,
Author = {Nguyen, Thu and Phan, Kim L and Kozakov, Dima and Gabelli, Sandra B and Kreitler, Dale F and Andrews, Lawrence C and Jakoncic, Jean and Sweet, Rober M and Soares, Alexei S and Bernstein, Herbert J},
Booktitle = {ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {INT UNION CRYSTALLOGRAPHY 2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND},
Pages = {C771--C771},
Title = {A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs},
Volume = {77},
Year = {2021}}

2020

S. Kotelnikov, A. Alekseenko, C. Liu, M. Ignatov, D. Padhorny, E. Brini, M. Lukin, E. Coutsias, K. A. Dill, and D. Kozakov, “Sampling and refinement protocols for template-based macrocycle docking: 2018 d3r grand challenge 4,” Journal of computer-aided molecular design, vol. 34, p. 179–189, 2020.
[BibTeX]

@article{kotelnikov2020sampling,
Author = {Kotelnikov, Sergei and Alekseenko, Andrey and Liu, Cong and Ignatov, Mikhail and Padhorny, Dzmitry and Brini, Emiliano and Lukin, Mark and Coutsias, Evangelos and Dill, Ken A and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of computer-aided molecular design},
Pages = {179--189},
Publisher = {Springer International Publishing},
Title = {Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4},
Volume = {34},
Year = {2020}}

J. Wang, A. Alekseenko, D. Kozakov, and Y. Miao, “Enhanced sampling of peptide binding to proteins through gaussian accelerated molecular dynamics simulations,” Biophysical journal, vol. 118, iss. 3, p. 139a, 2020.
[BibTeX]

@article{wang2020enhanced,
Author = {Wang, Jinan and Alekseenko, Andrey and Kozakov, Dima and Miao, Yinglong},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Biophysical Journal},
Number = {3},
Pages = {139a},
Publisher = {Elsevier},
Title = {Enhanced Sampling of Peptide Binding to Proteins through Gaussian Accelerated Molecular Dynamics Simulations},
Volume = {118},
Year = {2020}}

I. T. Desta, K. A. Porter, B. Xia, D. Kozakov, and S. Vajda, “Performance and its limits in rigid body protein-protein docking,” Structure, vol. 28, iss. 9, p. 1071–1081, 2020.
[BibTeX]

@article{desta2020performance,
Author = {Desta, Israel T and Porter, Kathryn A and Xia, Bing and Kozakov, Dima and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Structure},
Number = {9},
Pages = {1071--1081},
Publisher = {Elsevier},
Title = {Performance and its limits in rigid body protein-protein docking},
Volume = {28},
Year = {2020}}

D. Padhorny, K. A. Porter, M. Ignatov, A. Alekseenko, D. Beglov, S. Kotelnikov, R. Ashizawa, I. Desta, N. Alam, Z. Sun, and others, “Cluspro in rounds 38 to 45 of capri: toward combining template-based methods with free docking,” Proteins: structure, function, and bioinformatics, vol. 88, iss. 8, p. 1082–1090, 2020.
[BibTeX]

@article{padhorny2020cluspro,
Author = {Padhorny, Dzmitry and Porter, Kathryn A and Ignatov, Mikhail and Alekseenko, Andrey and Beglov, Dmitri and Kotelnikov, Sergei and Ashizawa, Ryota and Desta, Israel and Alam, Nawsad and Sun, Zhuyezi and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {8},
Pages = {1082--1090},
Publisher = {John Wiley \& Sons, Inc. Hoboken, USA},
Title = {ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking},
Volume = {88},
Year = {2020}}

A. Alekseenko, M. Ignatov, G. Jones, M. Sabitova, and D. Kozakov, “Protein–protein and protein–peptide docking with cluspro server,” Protein structure prediction, p. 157–174, 2020.
[BibTeX]

@article{alekseenko2020protein,
Author = {Alekseenko, Andrey and Ignatov, Mikhail and Jones, George and Sabitova, Maria and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Protein Structure Prediction},
Pages = {157--174},
Publisher = {Springer US},
Title = {Protein--protein and protein--peptide docking with ClusPro server},
Year = {2020}}

Z. Sun, I. Kolossváry, D. Kozakov, M. Sahin-Tóth, and S. Vajda, “The n34s mutation of spink1 may impact the kinetics of trypsinogen activation to cause early trypsin release in the pancreas,” Biorxiv, p. 2020–08, 2020.
[BibTeX]

@article{sun2020n34s,
Author = {Sun, Zhuyezi and Kolossv{\'a}ry, Istv{\'a}n and Kozakov, Dima and Sahin-T{\'o}th, Mikl{\'o}s and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {bioRxiv},
Pages = {2020--08},
Publisher = {Cold Spring Harbor Laboratory},
Title = {The N34S mutation of SPINK1 may impact the kinetics of trypsinogen activation to cause early trypsin release in the pancreas},
Year = {2020}}

@article{hekman2020actionable,
Author = {Hekman, Ryan M and Hume, Adam J and Goel, Raghuveera Kumar and Abo, Kristine M and Huang, Jessie and Blum, Benjamin C and Werder, Rhiannon B and Suder, Ellen L and Paul, Indranil and Phanse, Sadhna and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Molecular cell},
Number = {6},
Pages = {1104--1122},
Publisher = {Elsevier},
Title = {Actionable cytopathogenic host responses of human alveolar type 2 cells to SARS-CoV-2},
Volume = {80},
Year = {2020}}

A. E. Wakefield, C. Yueh, D. Beglov, M. S. Castilho, D. Kozakov, G. M. Keser{H u}, A. Whitty, and S. Vajda, “Benchmark sets for binding hot spot identification in fragment-based ligand discovery,” Journal of chemical information and modeling, vol. 60, iss. 12, p. 6612–6623, 2020.
[BibTeX]

@article{wakefield2020benchmark,
Author = {Wakefield, Amanda E and Yueh, Christine and Beglov, Dmitri and Castilho, Marcelo S and Kozakov, Dima and Keser{\H u}, Gy{\"o}rgy M and Whitty, Adrian and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of chemical information and modeling},
Number = {12},
Pages = {6612--6623},
Publisher = {American Chemical Society},
Title = {Benchmark sets for binding hot spot identification in fragment-based ligand discovery},
Volume = {60},
Year = {2020}}

I. V. Grebenkin, A. E. Alekseenko, N. A. Gaivoronskiy, M. G. Ignatov, A. M. Kazennov, D. Kozakov, A. P. Kulagin, Y. A. Kholodov, and others, “Ensemble building and statistical mechanics methods for mhc-peptide binding prediction,” Computer research and modeling, vol. 12, iss. 6, p. 1383–1395, 2020.
[BibTeX]

@article{grebenkin2020ensemble,
Author = {Grebenkin, Ivan V and Alekseenko, Andrey E and Gaivoronskiy, Nikolay A and Ignatov, Mikhail G and Kazennov, Andrey Maksimovich and Kozakov, DV and Kulagin, Andrey P and Kholodov, Yaroslav Aleksandrovich and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Computer research and modeling},
Number = {6},
Pages = {1383--1395},
Title = {Ensemble building and statistical mechanics methods for MHC-peptide binding prediction},
Volume = {12},
Year = {2020}}

G. Dignon, D. Kozakov, and K. A. Dill, “Computational design of excipient formulations for monoclonal antibody solutions,” in 2020 virtual aiche annual meeting, 2020.
[BibTeX]

@inproceedings{dignon2020computational,
Author = {Dignon, Gregory and Kozakov, Dima and Dill, Ken A},
Booktitle = {2020 Virtual AIChE Annual Meeting},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {AIChE},
Title = {Computational Design of Excipient Formulations for Monoclonal Antibody Solutions},
Year = {2020}}

A. Alekseenko, S. Kotelnikov, M. Ignatov, M. Egbert, Y. Kholodov, S. Vajda, and D. Kozakov, “Cluspro ligtbm: automated template-based small molecule docking,” Journal of molecular biology, vol. 432, iss. 11, p. 3404–3410, 2020.
[BibTeX]

@article{alekseenko2020cluspro,
Author = {Alekseenko, Andrey and Kotelnikov, Sergei and Ignatov, Mikhail and Egbert, Megan and Kholodov, Yaroslav and Vajda, Sandor and Kozakov, Dima},
Journal = {Journal of molecular biology},
Number = {11},
Pages = {3404--3410},
Publisher = {Academic Press},
Title = {ClusPro LigTBM: Automated template-based small molecule docking},
Volume = {432},
Year = {2020}}

A. Khramushin, O. Marcu, N. Alam, O. Shimony, D. Padhorny, E. Brini, K. A. Dill, S. Vajda, D. Kozakov, and O. Schueler-Furman, “Modeling beta-sheet peptide-protein interactions: rosetta flexpepdock in capri rounds 38-45,” Proteins: structure, function, and bioinformatics, vol. 88, iss. 8, p. 1037–1049, 2020.
[BibTeX]

@article{khramushin2020modeling,
Author = {Khramushin, Alisa and Marcu, Orly and Alam, Nawsad and Shimony, Orly and Padhorny, Dzmitry and Brini, Emiliano and Dill, Ken A and Vajda, Sandor and Kozakov, Dima and Schueler-Furman, Ora},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {8},
Pages = {1037--1049},
Publisher = {John Wiley \& Sons, Inc. Hoboken, USA},
Title = {Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45},
Volume = {88},
Year = {2020}}

2019

M. Ignatov, C. Liu, A. Alekseenko, Z. Sun, D. Padhorny, S. Kotelnikov, A. Kazennov, I. Grebenkin, Y. Kholodov, I. Kolosvari, and others, “Monte carlo on the manifold and md refinement for binding pose prediction of protein–ligand complexes: 2017 d3r grand challenge,” Journal of computer-aided molecular design, vol. 33, p. 119–127, 2019.
[BibTeX]

@article{ignatov2019monte,
Author = {Ignatov, Mikhail and Liu, Cong and Alekseenko, Andrey and Sun, Zhuyezi and Padhorny, Dzmitry and Kotelnikov, Sergei and Kazennov, Andrey and Grebenkin, Ivan and Kholodov, Yaroslav and Kolosvari, Istvan and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of computer-aided molecular design},
Pages = {119--127},
Publisher = {Springer International Publishing},
Title = {Monte Carlo on the manifold and MD refinement for binding pose prediction of protein--ligand complexes: 2017 D3R Grand Challenge},
Volume = {33},
Year = {2019}}

K. A. Porter, I. Desta, D. Kozakov, and S. Vajda, “What method to use for protein–protein docking?,” Current opinion in structural biology, vol. 55, p. 1–7, 2019.
[BibTeX]

@article{porter2019method,
Author = {Porter, Kathryn A and Desta, Israel and Kozakov, Dima and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Current Opinion in Structural Biology},
Pages = {1--7},
Publisher = {Elsevier Current Trends},
Title = {What method to use for protein--protein docking?},
Volume = {55},
Year = {2019}}

S. J. Wodak, E. Paci, N. V. Dokholyan, I. N. Berezovsky, A. Horovitz, J. Li, V. J. Hilser, I. Bahar, J. Karanicolas, G. Stock, and others, “Allostery in its many disguises: from theory to applications,” Structure, vol. 27, iss. 4, p. 566–578, 2019.
[BibTeX]

@article{wodak2019allostery,
Author = {Wodak, Shoshana J and Paci, Emanuele and Dokholyan, Nikolay V and Berezovsky, Igor N and Horovitz, Amnon and Li, Jing and Hilser, Vincent J and Bahar, Ivet and Karanicolas, John and Stock, Gerhard and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Structure},
Number = {4},
Pages = {566--578},
Publisher = {Elsevier},
Title = {Allostery in its many disguises: from theory to applications},
Volume = {27},
Year = {2019}}

E. Brini, D. Kozakov, and K. A. Dill, “Predicting protein dimer structures using meld$\times$ md,” Journal of chemical theory and computation, vol. 15, iss. 5, p. 3381–3389, 2019.
[BibTeX]

@article{brini2019predicting,
Author = {Brini, Emiliano and Kozakov, Dima and Dill, Ken A},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of chemical theory and computation},
Number = {5},
Pages = {3381--3389},
Publisher = {American Chemical Society},
Title = {Predicting protein dimer structures using MELD$\times$ MD},
Volume = {15},
Year = {2019}}

C. Yueh, J. Rettenmaier, B. Xia, D. R. Hall, A. Alekseenko, K. A. Porter, K. Barkovich, G. Keseru, A. Whitty, J. A. Wells, and others, “Kinase atlas: druggability analysis of potential allosteric sites in kinases,” Journal of medicinal chemistry, vol. 62, iss. 14, p. 6512–6524, 2019.
[BibTeX]

@article{yueh2019kinase,
Author = {Yueh, Christine and Rettenmaier, Justin and Xia, Bing and Hall, David R and Alekseenko, Andrey and Porter, Kathryn A and Barkovich, Krister and Keseru, Gyorgy and Whitty, Adrian and Wells, James A and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of medicinal chemistry},
Number = {14},
Pages = {6512--6524},
Publisher = {American Chemical Society},
Title = {Kinase atlas: druggability analysis of potential allosteric sites in kinases},
Volume = {62},
Year = {2019}}

M. Ignatov, E. Coutsias, and D. Kozakov, “Ultra-fast modeling of peptide-mhc interactions with 3d convolutional neural net,” in Journal of biomolecular structure & dynamics, 2019, p. 48–48.
[BibTeX]

@inproceedings{ignatov2019ultra,
Author = {Ignatov, Mikhail and Coutsias, Evangelos and Kozakov, Dima},
Booktitle = {JOURNAL OF BIOMOLECULAR STRUCTURE \& DYNAMICS},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {TAYLOR \& FRANCIS INC 530 WALNUT STREET, STE 850, PHILADELPHIA, PA 19106 USA},
Pages = {48--48},
Title = {Ultra-fast modeling of peptide-MHC interactions with 3D convolutional neural net},
Volume = {37},
Year = {2019}}

K. A. Porter, D. Padhorny, I. Desta, M. Ignatov, D. Beglov, S. Kotelnikov, Z. Sun, A. Alekseenko, I. Anishchenko, Q. Cong, and others, “Template-based modeling by cluspro in casp13 and the potential for using co-evolutionary information in docking,” Proteins: structure, function, and bioinformatics, vol. 87, iss. 12, p. 1241–1248, 2019.
[BibTeX]

@article{porter2019template,
Author = {Porter, Kathryn A and Padhorny, Dzmitry and Desta, Israel and Ignatov, Mikhail and Beglov, Dmitri and Kotelnikov, Sergei and Sun, Zhuyezi and Alekseenko, Andrey and Anishchenko, Ivan and Cong, Qian and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {12},
Pages = {1241--1248},
Publisher = {John Wiley \& Sons, Inc. Hoboken, USA},
Title = {Template-based modeling by ClusPro in CASP13 and the potential for using co-evolutionary information in docking},
Volume = {87},
Year = {2019}}

J. Wang, A. Alekseenko, D. Kozakov, and Y. Miao, “Improved modeling of peptide-protein binding through global docking and accelerated molecular dynamics simulations,” Frontiers in molecular biosciences, vol. 6, p. 112, 2019.
[BibTeX]

@article{wang2019improved,
Author = {Wang, Jinan and Alekseenko, Andrey and Kozakov, Dima and Miao, Yinglong},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Frontiers in molecular biosciences},
Pages = {112},
Publisher = {Frontiers Media SA},
Title = {Improved modeling of peptide-protein binding through global docking and accelerated molecular dynamics simulations},
Volume = {6},
Year = {2019}}

M. F. Lensink, G. Brysbaert, N. Nadzirin, S. Velankar, R. A. Chaleil, T. Gerguri, P. A. Bates, E. Laine, A. Carbone, S. Grudinin, and others, “Blind prediction of homo-and hetero-protein complexes: the casp13-capri experiment,” Proteins: structure, function, and bioinformatics, vol. 87, iss. 12, p. 1200–1221, 2019.
[BibTeX]

@article{lensink2019blind,
Author = {Lensink, Marc F and Brysbaert, Guillaume and Nadzirin, Nurul and Velankar, Sameer and Chaleil, Rapha{\"e}l AG and Gerguri, Tereza and Bates, Paul A and Laine, Elodie and Carbone, Alessandra and Grudinin, Sergei and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {12},
Pages = {1200--1221},
Publisher = {John Wiley \& Sons, Inc. Hoboken, USA},
Title = {Blind prediction of homo-and hetero-protein complexes: The CASP13-CAPRI experiment},
Volume = {87},
Year = {2019}}

M. Zhong, A. Lynch, S. N. Muellers, S. Jehle, L. Luo, D. R. Hall, R. Iwase, J. P. Carolan, M. Egbert, A. Wakefield, and others, “Interaction energetics and druggability of the protein–protein interaction between kelch-like ech-associated protein 1 (keap1) and nuclear factor erythroid 2 like 2 (nrf2),” Biochemistry, vol. 59, iss. 4, p. 563–581, 2019.
[BibTeX]

@article{zhong2019interaction,
Author = {Zhong, Mengqi and Lynch, Andrew and Muellers, Samantha N and Jehle, Stefan and Luo, Lingqi and Hall, David R and Iwase, Reina and Carolan, James P and Egbert, Megan and Wakefield, Amanda and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Biochemistry},
Number = {4},
Pages = {563--581},
Publisher = {American Chemical Society},
Title = {Interaction energetics and druggability of the protein--protein interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2)},
Volume = {59},
Year = {2019}}

S. Vajda, C. Yueh, and D. Kozakov, “Kinase atlas: predicted regulatory hot spots in kinases,” in Abstracts of papers of the american chemical society, 2019.
[BibTeX]

@inproceedings{vajda2019kinase,
Author = {Vajda, Sandor and Yueh, Christine and Kozakov, Dima},
Booktitle = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Title = {Kinase atlas: Predicted regulatory hot spots in kinases},
Volume = {258},
Year = {2019}}

@article{alekseenko2019cluspro,
Author = {Alekseenko, Andrey and Kotelnikov, Sergei and Ignatov, Mikhail and Egbert, Megan and Kholodov, Yaroslav and Vajda, Sandor and Kozakov, Dima},
Journal = {Journal of Molecular Biology},
Publisher = {Academic Press},
Title = {ClusPro LigTBM: Automated Template-Based Small Molecule Docking},
Year = {2019}}

@article{kotelnikov2019sampling,
Author = {Kotelnikov, Sergei and Alekseenko, Andrey and Liu, Cong and Ignatov, Mikhail and Padhorny, Dzmitry and Brini, Emiliano and Lukin, Mark and Coutsias, Evangelos and Dill, Ken A and Kozakov, Dima},
Journal = {Journal of Computer-Aided Molecular Design},
Pages = {1--11},
Publisher = {Springer International Publishing},
Title = {Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4},
Year = {2019}}

2018

D. Padhorny, D. R. Hall, H. Mirzaei, A. B. Mamonov, M. Moghadasi, A. Alekseenko, D. Beglov, and D. Kozakov, “Protein–ligand docking using fft based sampling: d3r case study,” Journal of computer-aided molecular design, vol. 32, p. 225–230, 2018.
[BibTeX]

@article{padhorny2018protein,
Author = {Padhorny, Dzmitry and Hall, David R and Mirzaei, Hanieh and Mamonov, Artem B and Moghadasi, Mohammad and Alekseenko, Andrey and Beglov, Dmitri and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of computer-aided molecular design},
Pages = {225--230},
Publisher = {Springer International Publishing},
Title = {Protein--ligand docking using FFT based sampling: D3R case study},
Volume = {32},
Year = {2018}}

D. Beglov, D. R. Hall, A. E. Wakefield, L. Luo, K. N. Allen, D. Kozakov, A. Whitty, and S. Vajda, “Exploring the structural origins of cryptic sites on proteins,” Proceedings of the national academy of sciences, vol. 115, iss. 15, p. E3416–E3425, 2018.
[BibTeX]

@article{beglov2018exploring,
Author = {Beglov, Dmitri and Hall, David R and Wakefield, Amanda E and Luo, Lingqi and Allen, Karen N and Kozakov, Dima and Whitty, Adrian and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Proceedings of the National Academy of Sciences},
Number = {15},
Pages = {E3416--E3425},
Publisher = {National Academy of Sciences},
Title = {Exploring the structural origins of cryptic sites on proteins},
Volume = {115},
Year = {2018}}

M. Ignatov, A. Kazennov, and D. Kozakov, “Cluspro fmft-saxs: ultra-fast filtering using small-angle x-ray scattering data in protein docking,” Journal of molecular biology, vol. 430, iss. 15, p. 2249–2255, 2018.
[BibTeX]

@article{ignatov2018cluspro,
Author = {Ignatov, Mikhail and Kazennov, Andrey and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of molecular biology},
Number = {15},
Pages = {2249--2255},
Publisher = {Academic Press},
Title = {ClusPro FMFT-SAXS: ultra-fast filtering using small-angle X-ray scattering data in protein docking},
Volume = {430},
Year = {2018}}

S. Zarbafian, M. Moghadasi, A. Roshandelpoor, F. Nan, K. Li, P. Vakli, S. Vajda, D. Kozakov, and I. C. Paschalidis, “Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes,” Scientific reports, vol. 8, iss. 1, p. 5896, 2018.
[BibTeX]

@article{zarbafian2018protein,
Author = {Zarbafian, Shahrooz and Moghadasi, Mohammad and Roshandelpoor, Athar and Nan, Feng and Li, Keyong and Vakli, Pirooz and Vajda, Sandor and Kozakov, Dima and Paschalidis, Ioannis Ch},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Scientific Reports},
Number = {1},
Pages = {5896},
Publisher = {Nature Publishing Group UK London},
Title = {Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes},
Volume = {8},
Year = {2018}}

O. G. Stasyk, I. O. Denega, D. Padhorny, K. V. Dmytruk, D. Kozakov, C. Abbas, and V. Stasyk, “Glucose regulation in the methylotrophic yeast hansenula (ogataea) polymorpha is mediated by a putative transceptor gcr1,” The international journal of biochemistry & cell biology, vol. 103, p. 25–34, 2018.
[BibTeX]

@article{stasyk2018glucose,
Author = {Stasyk, Olena G and Denega, Iryna O and Padhorny, Dzmitry and Dmytruk, Kostyantyn V and Kozakov, Dima and Abbas, Charles and Stasyk, V},
Journal = {The international journal of biochemistry \& cell biology},
Pages = {25--34},
Publisher = {Pergamon},
Title = {Glucose regulation in the methylotrophic yeast Hansenula (Ogataea) polymorpha is mediated by a putative transceptor Gcr1},
Volume = {103},
Year = {2018}}

2017

T. Bohnuud, L. Luo, S. J. Wodak, A. M. Bonvin, Z. Weng, S. Vajda, O. Schueler-Furman, and D. Kozakov, “A benchmark testing ground for integrating homology modeling and protein docking,” Proteins: structure, function, and bioinformatics, vol. 85, iss. 1, p. 10–16, 2017.
[BibTeX]

@article{bohnuud2017benchmark,
Author = {Bohnuud, Tanggis and Luo, Lingqi and Wodak, Shoshana J and Bonvin, Alexandre MJJ and Weng, Zhiping and Vajda, Sandor and Schueler-Furman, Ora and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {1},
Pages = {10--16},
Title = {A benchmark testing ground for integrating homology modeling and protein docking},
Volume = {85},
Year = {2017}}

S. Vajda, C. Yueh, D. Beglov, T. Bohnuud, S. E. Mottarella, B. Xia, D. R. Hall, and D. Kozakov, “New additions to the c lus p ro server motivated by capri,” Proteins: structure, function, and bioinformatics, vol. 85, iss. 3, p. 435–444, 2017.
[BibTeX]

@article{vajda2017new,
Author = {Vajda, Sandor and Yueh, Christine and Beglov, Dmitri and Bohnuud, Tanggis and Mottarella, Scott E and Xia, Bing and Hall, David R and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {3},
Pages = {435--444},
Title = {New additions to the C lus P ro server motivated by CAPRI},
Volume = {85},
Year = {2017}}

O. Marcu, E. Dodson, N. Alam, M. Sperber, D. Kozakov, M. F. Lensink, and O. Schueler-Furman, “Flexpepdock lessons from capri peptide–protein rounds and suggested new criteria for assessment of model quality and utility,” Proteins: structure, function, and bioinformatics, vol. 85, iss. 3, p. 445–462, 2017.
[BibTeX]

@article{marcu2017flexpepdock,
Author = {Marcu, Orly and Dodson, Emma-Joy and Alam, Nawsad and Sperber, Michal and Kozakov, Dima and Lensink, Marc F and Schueler-Furman, Ora},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {3},
Pages = {445--462},
Title = {FlexPepDock lessons from CAPRI peptide--protein rounds and suggested new criteria for assessment of model quality and utility},
Volume = {85},
Year = {2017}}

D. Kozakov, D. R. Hall, B. Xia, K. A. Porter, D. Padhorny, C. Yueh, D. Beglov, and S. Vajda, “The cluspro web server for protein–protein docking,” Nature protocols, vol. 12, iss. 2, p. 255–278, 2017.
[BibTeX]

@article{kozakov2017cluspro,
Author = {Kozakov, Dima and Hall, David R and Xia, Bing and Porter, Kathryn A and Padhorny, Dzmitry and Yueh, Christine and Beglov, Dmitri and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Nature protocols},
Number = {2},
Pages = {255--278},
Publisher = {Nature Publishing Group},
Title = {The ClusPro web server for protein--protein docking},
Volume = {12},
Year = {2017}}

T. Bohnuud, G. Jones, O. Schueler-Furman, and D. Kozakov, “Detection of peptide-binding sites on protein surfaces using the peptimap server,” Modeling peptide-protein interactions: methods and protocols, p. 11–20, 2017.
[BibTeX]

@article{bohnuud2017detection,
Author = {Bohnuud, Tanggis and Jones, George and Schueler-Furman, Ora and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Modeling Peptide-Protein Interactions: Methods and Protocols},
Pages = {11--20},
Publisher = {Springer New York},
Title = {Detection of peptide-binding sites on protein surfaces using the PeptiMap server},
Year = {2017}}

K. A. Porter, B. Xia, D. Beglov, T. Bohnuud, N. Alam, O. Schueler-Furman, and D. Kozakov, “Cluspro peptidock: efficient global docking of peptide recognition motifs using fft,” Bioinformatics, vol. 33, iss. 20, p. 3299–3301, 2017.
[BibTeX]

@article{porter2017cluspro,
Author = {Porter, Kathryn A and Xia, Bing and Beglov, Dmitri and Bohnuud, Tanggis and Alam, Nawsad and Schueler-Furman, Ora and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Bioinformatics},
Number = {20},
Pages = {3299--3301},
Publisher = {Oxford University Press},
Title = {ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT},
Volume = {33},
Year = {2017}}

N. Alam, D. Kozakov, and O. Schueler-Furman, “High-resolution modeling of peptide-protein interactions using a fragment-based global docking approach, piper-flexpepdock,” in Febs journal, 2017, p. 317–317.
[BibTeX]

@inproceedings{alam2017high,
Author = {Alam, N and Kozakov, D and Schueler-Furman, O},
Booktitle = {Febs Journal},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {WILEY 111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Pages = {317--317},
Title = {High-resolution modeling of peptide-protein interactions using a fragment-based global docking approach, PIPER-FlexPepDock},
Volume = {284},
Year = {2017}}

S. Vajda, D. Kozakov, and D. Hall, “Prediction on allosteric and cryptic sites on ligand-free protein structures,” in Abstracts of papers of the american chemical society, 2017.
[BibTeX]

@inproceedings{vajda2017prediction,
Author = {Vajda, Sandor and Kozakov, Dima and Hall, David},
Booktitle = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Title = {Prediction on allosteric and cryptic sites on ligand-free protein structures},
Volume = {253},
Year = {2017}}

D. Kozakov, “Kinase allostery atlas,” in Abstracts of papers of the american chemical society, 2017.
[BibTeX]

@inproceedings{kozakov2017kinase,
Author = {Kozakov, Dima},
Booktitle = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Title = {Kinase allostery atlas},
Volume = {253},
Year = {2017}}

C. Yueh, D. R. Hall, B. Xia, D. Padhorny, D. Kozakov, and S. Vajda, “Cluspro-dc: dimer classification by the cluspro server for protein–protein docking,” Journal of molecular biology, vol. 429, iss. 3, p. 372–381, 2017.
[BibTeX]

@article{yueh2017cluspro,
Author = {Yueh, Christine and Hall, David R and Xia, Bing and Padhorny, Dzmitry and Kozakov, Dima and Vajda, Sandor},
Journal = {Journal of molecular biology},
Number = {3},
Pages = {372--381},
Publisher = {Academic Press},
Title = {ClusPro-DC: Dimer classification by the CLUSPRO server for protein--protein docking},
Volume = {429},
Year = {2017}}

2016

A. B. Mamonov, M. Moghadasi, H. Mirzaei, S. Zarbafian, L. E. Grove, T. Bohnuud, P. Vakili, I. Ch. Paschalidis, S. Vajda, and D. Kozakov, “Focused grid-based resampling for protein docking and mapping,” Journal of computational chemistry, vol. 37, iss. 11, p. 961–970, 2016.
[BibTeX]

@article{mamonov2016focused,
Author = {Mamonov, Artem B and Moghadasi, Mohammad and Mirzaei, Hanieh and Zarbafian, Shahrooz and Grove, Laurie E and Bohnuud, Tanggis and Vakili, Pirooz and Ch. Paschalidis, Ioannis and Vajda, Sandor and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of computational chemistry},
Number = {11},
Pages = {961--970},
Title = {Focused grid-based resampling for protein docking and mapping},
Volume = {37},
Year = {2016}}

M. F. Lensink, S. Velankar, A. Kryshtafovych, S. Huang, D. Schneidman-Duhovny, A. Sali, J. Segura, N. Fernandez-Fuentes, S. Viswanath, R. Elber, and others, “Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: a casp-capri experiment,” Proteins: structure, function, and bioinformatics, vol. 84, p. 323–348, 2016.
[BibTeX]

@article{lensink2016prediction,
Author = {Lensink, Marc F and Velankar, Sameer and Kryshtafovych, Andriy and Huang, Shen-You and Schneidman-Duhovny, Dina and Sali, Andrej and Segura, Joan and Fernandez-Fuentes, Narcis and Viswanath, Shruthi and Elber, Ron and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Pages = {323--348},
Title = {Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment},
Volume = {84},
Year = {2016}}

B. Xia, S. Vajda, and D. Kozakov, “Accounting for pairwise distance restraints in fft-based protein–protein docking,” Bioinformatics, vol. 32, iss. 21, p. 3342–3344, 2016.
[BibTeX]

@article{xia2016accounting,
Author = {Xia, Bing and Vajda, Sandor and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Bioinformatics},
Number = {21},
Pages = {3342--3344},
Publisher = {Oxford University Press},
Title = {Accounting for pairwise distance restraints in FFT-based protein--protein docking},
Volume = {32},
Year = {2016}}

D. Padhorny, A. Kazennov, B. S. Zerbe, K. A. Porter, B. Xia, S. E. Mottarella, Y. Kholodov, D. W. Ritchie, S. Vajda, and D. Kozakov, “Protein–protein docking by fast generalized fourier transforms on 5d rotational manifolds,” Proceedings of the national academy of sciences, vol. 113, iss. 30, p. E4286–E4293, 2016.
[BibTeX]

@article{padhorny2016protein,
Author = {Padhorny, Dzmitry and Kazennov, Andrey and Zerbe, Brandon S and Porter, Kathryn A and Xia, Bing and Mottarella, Scott E and Kholodov, Yaroslav and Ritchie, David W and Vajda, Sandor and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Proceedings of the National Academy of Sciences},
Number = {30},
Pages = {E4286--E4293},
Publisher = {National Academy of Sciences},
Title = {Protein--protein docking by fast generalized Fourier transforms on 5D rotational manifolds},
Volume = {113},
Year = {2016}}

O. Schueler-Furman, N. Alam, O. Marcu, E. Dodson, J. Fahoum, S. Rotem-Bamberger, and D. Kozakov, “The versatile roles of peptide-mediated interactions detected by modeling and experiment,” in Febs journal, 2016, p. 23–23.
[BibTeX]

@inproceedings{schueler2016versatile,
Author = {Schueler-Furman, O and Alam, N and Marcu, O and Dodson, E and Fahoum, J and Rotem-Bamberger, S and Kozakov, D},
Booktitle = {FEBS JOURNAL},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {WILEY-BLACKWELL 111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Pages = {23--23},
Title = {The versatile roles of peptide-mediated interactions detected by modeling and experiment},
Volume = {283},
Year = {2016}}

C. Yueh, D. Kozakov, and S. Vajda, “Analysis of protein aggregation by docking,” in Abstracts of papers of the american chemical society, 2016.
[BibTeX]

@inproceedings{yueh2016analysis,
Author = {Yueh, Christine and Kozakov, Dima and Vajda, Sandor},
Booktitle = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Title = {Analysis of protein aggregation by docking},
Volume = {251},
Year = {2016}}

K. Porter, B. Xia, D. Beglov, O. Furman, and D. Kozakov, “Efficient global peptide docking using motif-derived fragments,” in Abstracts of papers of the american chemical society, 2016.
[BibTeX]

@inproceedings{porter2016efficient,
Author = {Porter, Kathryn and Xia, Bing and Beglov, Dmitri and Furman, Ora and Kozakov, Dima},
Booktitle = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Title = {Efficient global peptide docking using motif-derived fragments},
Volume = {251},
Year = {2016}}

D. Kozakov, S. Mottarella, and S. Vajda, “Statistical mechanics of protein-protein association,” in Abstracts of papers of the american chemical society, 2016.
[BibTeX]

@inproceedings{kozakov2016statistical,
Author = {Kozakov, Dima and Mottarella, Scott and Vajda, Sandor},
Booktitle = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Title = {Statistical mechanics of protein-protein association},
Volume = {251},
Year = {2016}}

L. E. Grove, S. Vajda, and D. Kozakov, “Computational methods to support fragment-based drug discovery,” Fragment-based drug discovery lessons and outlook, p. 197–222, 2016.
[BibTeX]

@article{grove2016computational,
Author = {Grove, Laurie E and Vajda, Sandor and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Fragment-based Drug Discovery Lessons and Outlook},
Pages = {197--222},
Publisher = {Wiley-VCH Verlag GmbH \& Co. KGaA Weinheim, Germany},
Title = {Computational Methods to Support Fragment-based Drug Discovery},
Year = {2016}}

2015

D. Kozakov, L. E. Grove, D. R. Hall, T. Bohnuud, S. E. Mottarella, L. Luo, B. Xia, D. Beglov, and S. Vajda, “The ftmap family of web servers for determining and characterizing ligand-binding hot spots of proteins,” Nature protocols, vol. 10, iss. 5, p. 733–755, 2015.
[BibTeX]

@article{kozakov2015ftmap,
Author = {Kozakov, Dima and Grove, Laurie E and Hall, David R and Bohnuud, Tanggis and Mottarella, Scott E and Luo, Lingqi and Xia, Bing and Beglov, Dmitri and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Nature protocols},
Number = {5},
Pages = {733--755},
Publisher = {Nature Publishing Group UK London},
Title = {The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins},
Volume = {10},
Year = {2015}}

D. Kozakov, D. R. Hall, S. Jehle, L. Luo, S. O. Ochiana, E. V. Jones, M. Pollastri, K. N. Allen, A. Whitty, and S. Vajda, “Ligand deconstruction: why some fragment binding positions are conserved and others are not,” Proceedings of the national academy of sciences, vol. 112, iss. 20, p. E2585–E2594, 2015.
[BibTeX]

@article{kozakov2015ligand,
Author = {Kozakov, Dima and Hall, David R and Jehle, Stefan and Luo, Lingqi and Ochiana, Stefan O and Jones, Elizabeth V and Pollastri, Michael and Allen, Karen N and Whitty, Adrian and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Proceedings of the National Academy of Sciences},
Number = {20},
Pages = {E2585--E2594},
Publisher = {National Academy of Sciences},
Title = {Ligand deconstruction: Why some fragment binding positions are conserved and others are not},
Volume = {112},
Year = {2015}}

B. Xia, A. Mamonov, S. Leysen, K. N. Allen, S. V. Strelkov, I. C. Paschalidis, S. Vajda, and D. Kozakov, Accounting for observed small angle x-ray scattering profile in the protein–protein docking server cluspro, 2015.
[BibTeX]

@misc{xia2015accounting,
Author = {Xia, Bing and Mamonov, Artem and Leysen, Seppe and Allen, Karen N and Strelkov, Sergei V and Paschalidis, Ioannis Ch and Vajda, Sandor and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Title = {Accounting for observed small angle X-ray scattering profile in the protein--protein docking server cluspro},
Year = {2015}}

M. Zhong, A. Lynch, S. Jehle, D. Kozakov, S. Vajda, K. Allen, and A. Whitty, “Fragment-based drug discovery targeting keap1/nrf2 binding,” The faseb journal, vol. 29, p. 712–20, 2015.
[BibTeX]

@article{zhong2015fragment,
Author = {Zhong, Mengqi and Lynch, Andrew and Jehle, Stefan and Kozakov, Dima and Vajda, Sandor and Allen, Karen and Whitty, Adrian},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {The FASEB Journal},
Pages = {712--20},
Publisher = {The Federation of American Societies for Experimental Biology},
Title = {Fragment-based Drug Discovery Targeting KEAP1/Nrf2 Binding},
Volume = {29},
Year = {2015}}

A. Kazennov, A. Alekseenko, D. Kozakov, D. Padhorny, and Y. Kholodov, “Efficient search for the possible mutual arrangements of two rigid bodies with the use of the generalized five-dimensional fourier transform,” Mathematical models and computer simulations, vol. 7, p. 315–322, 2015.
[BibTeX]

@article{kazennov2015efficient,
Author = {Kazennov, AM and Alekseenko, AE and Kozakov, D and Padhorny, DN and Kholodov, YA},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Mathematical Models and Computer Simulations},
Pages = {315--322},
Publisher = {Pleiades Publishing},
Title = {Efficient search for the possible mutual arrangements of two rigid bodies with the use of the generalized five-dimensional Fourier transform},
Volume = {7},
Year = {2015}}

H. Mirzaei, S. Zarbafian, E. Villar, S. Mottarella, D. Beglov, S. Vajda, I. C. Paschalidis, P. Vakili, and D. Kozakov, “Energy minimization on manifolds for docking flexible molecules,” Journal of chemical theory and computation, vol. 11, iss. 3, p. 1063–1076, 2015.
[BibTeX]

@article{mirzaei2015energy,
Author = {Mirzaei, Hanieh and Zarbafian, Shahrooz and Villar, Elizabeth and Mottarella, Scott and Beglov, Dmitri and Vajda, Sandor and Paschalidis, Ioannis Ch and Vakili, Pirooz and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of chemical theory and computation},
Number = {3},
Pages = {1063--1076},
Publisher = {American Chemical Society},
Title = {Energy minimization on manifolds for docking flexible molecules},
Volume = {11},
Year = {2015}}

M. Moghadasi, H. Mirzaei, A. Mamonov, P. Vakili, S. Vajda, I. C. Paschalidis, and D. Kozakov, “The impact of side-chain packing on protein docking refinement,” Journal of chemical information and modeling, vol. 55, iss. 4, p. 872–881, 2015.
[BibTeX]

@article{moghadasi2015impact,
Author = {Moghadasi, Mohammad and Mirzaei, Hanieh and Mamonov, Artem and Vakili, Pirooz and Vajda, Sandor and Paschalidis, Ioannis Ch and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of chemical information and modeling},
Number = {4},
Pages = {872--881},
Publisher = {American Chemical Society},
Title = {The impact of side-chain packing on protein docking refinement},
Volume = {55},
Year = {2015}}

N. Alam, A. Lavi, N. London, B. Raveh, D. Kozakov, and O. Schueler-Furman, “180 towards the high-resolution, ab initio modeling of peptide-mediated interactions,” Journal of biomolecular structure and dynamics, vol. 33, iss. sup1, p. 117–118, 2015.
[BibTeX]

@article{alam2015180,
Author = {Alam, Nawsad and Lavi, Assaf and London, Nir and Raveh, Barak and Kozakov, Dima and Schueler-Furman, Ora},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of Biomolecular Structure and Dynamics},
Number = {sup1},
Pages = {117--118},
Publisher = {Taylor \& Francis},
Title = {180 Towards the high-resolution, ab initio modeling of peptide-mediated interactions},
Volume = {33},
Year = {2015}}

D. Kozakov, D. R. Hall, R. L. Napoleon, C. Yueh, A. Whitty, and S. Vajda, “New frontiers in druggability,” Journal of medicinal chemistry, vol. 58, iss. 23, p. 9063–9088, 2015.
[BibTeX]

@article{kozakov2015new,
Author = {Kozakov, Dima and Hall, David R and Napoleon, Raeanne L and Yueh, Christine and Whitty, Adrian and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Journal of Medicinal Chemistry},
Number = {23},
Pages = {9063--9088},
Publisher = {American Chemical Society},
Title = {New frontiers in druggability},
Volume = {58},
Year = {2015}}

S. Vajda, A. Whitty, and D. Kozakov, “Fragments and hot spots in drug discovery,” Oncotarget, vol. 6, iss. 22, p. 18740, 2015.
[BibTeX]

@article{vajda2015fragments,
Author = {Vajda, Sandor and Whitty, Adrian and Kozakov, Dima},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Oncotarget},
Number = {22},
Pages = {18740},
Publisher = {Impact Journals, LLC},
Title = {Fragments and hot spots in drug discovery},
Volume = {6},
Year = {2015}}

D. R. Hall, D. Kozakov, A. Whitty, and S. Vajda, “Lessons from hot spot analysis for fragment-based drug discovery,” Trends in pharmacological sciences, vol. 36, iss. 11, p. 724–736, 2015.
[BibTeX]

@article{hall2015lessons,
Author = {Hall, David R and Kozakov, Dima and Whitty, Adrian and Vajda, Sandor},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Trends in pharmacological sciences},
Number = {11},
Pages = {724--736},
Publisher = {Elsevier},
Title = {Lessons from hot spot analysis for fragment-based drug discovery},
Volume = {36},
Year = {2015}}

V. Lukose, L. Luo, D. Kozakov, S. Vajda, K. N. Allen, and B. Imperiali, “Conservation and covariance in small bacterial phosphoglycosyltransferases identify the functional catalytic core,” Biochemistry, vol. 54, iss. 50, p. 7326–7334, 2015.
[BibTeX]

@article{lukose2015conservation,
Author = {Lukose, Vinita and Luo, Lingqi and Kozakov, Dima and Vajda, Sandor and Allen, Karen N and Imperiali, Barbara},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Biochemistry},
Number = {50},
Pages = {7326--7334},
Publisher = {American Chemical Society},
Title = {Conservation and covariance in small bacterial phosphoglycosyltransferases identify the functional catalytic core},
Volume = {54},
Year = {2015}}

Z. Sun, D. Beglov, D. Kozakov, D. Hall, and S. Vajda, “Developing the benchmark for protein macrocycle docking,” in Abstracts of papers of the american chemical society, 2015.
[BibTeX]

@inproceedings{sun2015developing,
Author = {Sun, Zhuyezi and Beglov, Dmitri and Kozakov, Dmytro and Hall, David and Vajda, Sandor},
Booktitle = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Title = {Developing the benchmark for protein macrocycle docking},
Volume = {250},
Year = {2015}}

D. Padhorny, A. Kazennov, K. Porter, D. Hall, D. Ritchie, and D. Kozakov, “Fast fourier transform sampling on the manifolds for modeling protein-protein interactions,” in Abstracts of papers of the american chemical society, 2015.
[BibTeX]

@inproceedings{padhorny2015fast,
Author = {Padhorny, Dzmitry and Kazennov, Andrey and Porter, Kathryn and Hall, David and Ritchie, David and Kozakov, Dmytro},
Booktitle = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Title = {Fast Fourier Transform sampling on the manifolds for modeling protein-protein interactions},
Volume = {250},
Year = {2015}}

K. Porter, D. Beglov, N. Alam, O. Schueler-Furman, and D. Kozakov, “Prediction of peptide-protein interactions using motif-derived fragments,” in Abstracts of papers of the american chemical society, 2015.
[BibTeX]

@inproceedings{porter2015prediction,
Author = {Porter, Kathryn and Beglov, Dmitri and Alam, Nawsad and Schueler-Furman, Ora and Kozakov, Dmytro},
Booktitle = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Title = {Prediction of peptide-protein interactions using motif-derived fragments},
Volume = {250},
Year = {2015}}

S. Vajda, D. Kozakov, P. Vakili, and I. Paschalidis, “Exploring dimensionality reduction in protein-protein association,” in Abstracts of papers of the american chemical society, 2015.
[BibTeX]

@inproceedings{vajda2015exploring,
Author = {Vajda, Sandor and Kozakov, Dmytro and Vakili, Pirooz and Paschalidis, Ioannis},
Booktitle = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Title = {Exploring dimensionality reduction in protein-protein association},
Volume = {250},
Year = {2015}}

B. Xia, S. Vajda, and D. Kozakov, “Fast ftflex: efficient computational solvent mapping with flexible sidechains,” in Abstracts of papers of the american chemical society, 2015.
[BibTeX]

@inproceedings{xia2015fast,
Author = {Xia, Bing and Vajda, Sandor and Kozakov, Dmytro},
Booktitle = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Title = {Fast FTFlex: Efficient computational solvent mapping with flexible sidechains},
Volume = {250},
Year = {2015}}

L. Vinita, L. Lingqi, K. Dima, V. Sandor, I. Barbara, and others, “Conservation and covariance in small bacterial phosphoglycosyltransferases identify the functional catalytic core,” , 2015.
[BibTeX]

@article{vinita2015conservation,
Author = {Vinita, Lukose and Lingqi, Luo and Dima, Kozakov and Sandor, Vajda and Barbara, Imperiali and others},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Title = {Conservation and Covariance in Small Bacterial Phosphoglycosyltransferases Identify the Functional Catalytic Core},
Year = {2015}}

D. Kozakov, “Grove le hall dr bohnuud t. mottarella se luo l. xia b. beglov d. vajda s,” Nat. protoc, vol. 10, p. 733–755, 2015.
[BibTeX]

@article{kozakov2015grove,
Author = {Kozakov, D},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Journal = {Nat. Protoc},
Pages = {733--755},
Title = {Grove LE Hall DR Bohnuud T. Mottarella SE Luo L. Xia B. Beglov D. Vajda S},
Volume = {10},
Year = {2015}}

D. Kozakov, P. Vakili, I. C. Paschalidis, and S. Vajda, “Encounter complexes and dimensionality reduction in protein-protein association,” in Journal of biomolecular structure & dynamics, 2015, p. 32–32.
[BibTeX]

@inproceedings{kozakov2015encounter,
Author = {Kozakov, Dima and Vakili, Pirooz and Paschalidis, Ioannis Ch and Vajda, Sandor},
Booktitle = {JOURNAL OF BIOMOLECULAR STRUCTURE \& DYNAMICS},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {TAYLOR \& FRANCIS INC 530 WALNUT STREET, STE 850, PHILADELPHIA, PA 19106 USA},
Pages = {32--32},
Title = {Encounter complexes and dimensionality reduction in protein-protein association},
Volume = {33},
Year = {2015}}

R. Mannhold, H. Kubinyi, and G. Folkers, Fragment-based drug discovery: lessons and outlookJohn Wiley & Sons, 2015.
[BibTeX]

@misc{mannhold2015fragment,
Author = {Mannhold, Raimund and Kubinyi, Hugo and Folkers, Gerd},
Publisher = {John Wiley \& Sons},
Title = {Fragment-based drug discovery: lessons and outlook},
Year = {2015}}

2014

F. Nan, M. Moghadasi, P. Vakili, S. Vajda, D. Kozakov, and I. C. Paschalidis, “A subspace semi-definite programming-based underestimation (ssdu) method for stochastic global optimization in protein docking,” in 53rd ieee conference on decision and control, 2014, p. 4623–4628.
[BibTeX]

@inproceedings{nan2014subspace,
Author = {Nan, Feng and Moghadasi, Mohammad and Vakili, Pirooz and Vajda, Sandor and Kozakov, Dima and Paschalidis, Ioannis Ch},
Booktitle = {53rd IEEE Conference on Decision and Control},
Date-Added = {2023-09-28 14:23:37 +0000},
Date-Modified = {2023-09-28 14:23:37 +0000},
Organization = {IEEE},
Pages = {4623--4628},
Title = {A subspace semi-definite programming-based underestimation (ssdu) method for stochastic global optimization in protein docking},
Year = {2014}}

E. A. Villar, D. Beglov, S. Chennamadhavuni, J. A. Porco Jr, D. Kozakov, S. Vajda, and A. Whitty, “How proteins bind macrocycles,” Nature chemical biology, vol. 10, iss. 9, p. 723, 2014.
[BibTeX]

@article{villar2014proteins,
Author = {Villar, Elizabeth A and Beglov, Dmitri and Chennamadhavuni, Spandan and Porco Jr, John A and Kozakov, Dima and Vajda, Sandor and Whitty, Adrian},
Journal = {Nature chemical biology},
Number = {9},
Pages = {723},
Publisher = {Nature Publishing Group},
Title = {How proteins bind macrocycles},
Volume = {10},
Year = {2014}}

M. F. Lensink, I. H. Moal, P. A. Bates, P. L. Kastritis, A. S. Melquiond, E. Karaca, C. Schmitz, M. Van Dijk, A. M. Bonvin, M. Eisenstein, and others, “Blind prediction of interfacial water positions in capri,” Proteins: structure, function, and bioinformatics, vol. 82, iss. 4, p. 620–632, 2014.
[BibTeX]

@article{lensink2014blind,
Author = {Lensink, Marc F and Moal, Iain H and Bates, Paul A and Kastritis, Panagiotis L and Melquiond, Adrien SJ and Karaca, Ezgi and Schmitz, Christophe and Van Dijk, Marc and Bonvin, Alexandre MJJ and Eisenstein, Miriam and others},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {4},
Pages = {620--632},
Title = {Blind prediction of interfacial water positions in CAPRI},
Volume = {82},
Year = {2014}}

H. K. Pillai, M. Fang, D. Beglov, D. Kozakov, S. Vajda, H. M. Stapleton, T. F. Webster, and J. J. Schlezinger, “Ligand binding and activation of ppar $\gamma$ by firemaster\textregistered 550: effects on adipogenesis and osteogenesis in vitro,” Environmental health perspectives, vol. 122, iss. 11, p. 1225–1232, 2014.
[BibTeX]

@article{pillai2014ligand,
Author = {Pillai, Hari K and Fang, Mingliang and Beglov, Dmitri and Kozakov, Dima and Vajda, Sandor and Stapleton, Heather M and Webster, Thomas F and Schlezinger, Jennifer J},
Journal = {Environmental health perspectives},
Number = {11},
Pages = {1225--1232},
Publisher = {NLM-Export},
Title = {Ligand Binding and Activation of PPAR $\gamma$ by Firemaster{\textregistered} 550: Effects on Adipogenesis and Osteogenesis in Vitro},
Volume = {122},
Year = {2014}}

E. Yakubovskaya, K. E. Guja, E. T. Eng, W. S. Choi, E. Mejia, D. Beglov, M. Lukin, D. Kozakov, and M. Garcia-Diaz, “Organization of the human mitochondrial transcription initiation complex,” Nucleic acids research, vol. 42, iss. 6, p. 4100–4112, 2014.
[BibTeX]

@article{yakubovskaya2014organization,
Author = {Yakubovskaya, Elena and Guja, Kip E and Eng, Edward T and Choi, Woo Suk and Mejia, Edison and Beglov, Dmitri and Lukin, Mark and Kozakov, Dima and Garcia-Diaz, Miguel},
Journal = {Nucleic acids research},
Number = {6},
Pages = {4100--4112},
Publisher = {Oxford University Press},
Title = {Organization of the human mitochondrial transcription initiation complex},
Volume = {42},
Year = {2014}}

D. Kozakov, K. Li, D. R. Hall, D. Beglov, J. Zheng, P. Vakili, O. Schueler-Furman, I. C. Paschalidis, M. G. Clore, and S. Vajda, “Encounter complexes and dimensionality reduction in protein–protein association,” Elife, vol. 3, p. e01370, 2014.
[BibTeX]

@article{kozakov2014encounter,
Author = {Kozakov, Dima and Li, Keyong and Hall, David R and Beglov, Dmitri and Zheng, Jiefu and Vakili, Pirooz and Schueler-Furman, Ora and Paschalidis, Ioannis Ch and Clore, G Marius and Vajda, Sandor},
Journal = {Elife},
Pages = {e01370},
Publisher = {eLife Sciences Publications Limited},
Title = {Encounter complexes and dimensionality reduction in protein--protein association},
Volume = {3},
Year = {2014}}

T. Bohnuud, D. Kozakov, and S. Vajda, “Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces,” Plos computational biology, vol. 10, iss. 10, p. e1003872, 2014.
[BibTeX]

@article{bohnuud2014evidence,
Author = {Bohnuud, Tanggis and Kozakov, Dima and Vajda, Sandor},
Journal = {PLoS computational biology},
Number = {10},
Pages = {e1003872},
Publisher = {Public Library of Science},
Title = {Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces},
Volume = {10},
Year = {2014}}

A. M. Bogorad, B. Xia, D. G. Sandor, A. B. Mamonov, T. R. Cafarella, S. Jehle, S. Vajda, D. Kozakov, and A. Marintchev, “Insights into the architecture of the eif2b$\alpha$/$\beta$/$\delta$ regulatory subcomplex,” Biochemistry, vol. 53, iss. 21, p. 3432–3445, 2014.
[BibTeX]

@article{bogorad2014insights,
Author = {Bogorad, Andrew M and Xia, Bing and Sandor, Dana G and Mamonov, Artem B and Cafarella, Tanya R and Jehle, Stefan and Vajda, Sandor and Kozakov, Dima and Marintchev, Assen},
Journal = {Biochemistry},
Number = {21},
Pages = {3432--3445},
Publisher = {American Chemical Society},
Title = {Insights into the architecture of the eIF2B$\alpha$/$\beta$/$\delta$ regulatory subcomplex},
Volume = {53},
Year = {2014}}

S. E. Mottarella, D. Beglov, N. Beglova, M. A. Nugent, D. Kozakov, and S. Vajda, “Docking server for the identification of heparin binding sites on proteins,” Journal of chemical information and modeling, vol. 54, iss. 7, p. 2068–2078, 2014.
[BibTeX]

@article{mottarella2014docking,
Author = {Mottarella, Scott E and Beglov, Dmitri and Beglova, Natalia and Nugent, Matthew A and Kozakov, Dima and Vajda, Sandor},
Journal = {Journal of chemical information and modeling},
Number = {7},
Pages = {2068--2078},
Publisher = {American Chemical Society},
Title = {Docking server for the identification of heparin binding sites on proteins},
Volume = {54},
Year = {2014}}

P. Vakili, H. Mirzaei, S. Zarbafian, I. C. Paschalidis, D. Kozakov, and S. Vajda, “Optimization on the space of rigid and flexible motions: an alternative manifold optimization approach,” in 53rd ieee conference on decision and control, 2014, p. 5825–5830.
[BibTeX]

@inproceedings{vakili2014optimization,
Author = {Vakili, Pirooz and Mirzaei, Hanieh and Zarbafian, Shahrooz and Paschalidis, Ioannis Ch and Kozakov, Dima and Vajda, Sandor},
Booktitle = {53rd IEEE Conference on Decision and Control},
Organization = {IEEE},
Pages = {5825--5830},
Title = {Optimization on the space of rigid and flexible motions: an alternative manifold optimization approach},
Year = {2014}}

R. Chowdhury, D. Beglov, M. Moghadasi, I. C. Paschalidis, P. Vakili, S. Vajda, C. Bajaj, and D. Kozakov, “Efficient maintenance and update of nonbonded lists in macromolecular simulations,” Journal of chemical theory and computation, vol. 10, iss. 10, p. 4449–4454, 2014.
[BibTeX]

@article{chowdhury2014efficient,
Author = {Chowdhury, Rezaul and Beglov, Dmitri and Moghadasi, Mohammad and Paschalidis, Ioannis Ch and Vakili, Pirooz and Vajda, Sandor and Bajaj, Chandrajit and Kozakov, Dima},
Journal = {Journal of chemical theory and computation},
Number = {10},
Pages = {4449--4454},
Publisher = {American Chemical Society},
Title = {Efficient maintenance and update of nonbonded lists in macromolecular simulations},
Volume = {10},
Year = {2014}}

U. Shin, D. E. Williams, D. Kozakov, D. R. Hall, D. Beglov, S. Vajda, R. J. Andersen, and J. Pelletier, “Stimulators of translation identified during a small molecule screening campaign,” Analytical biochemistry, vol. 447, p. 6–14, 2014.
[BibTeX]

@article{shin2014stimulators,
Author = {Shin, Unkyung and Williams, David E and Kozakov, Dima and Hall, David R and Beglov, Dmitri and Vajda, Sandor and Andersen, Raymond J and Pelletier, Jerry},
Journal = {Analytical biochemistry},
Pages = {6--14},
Publisher = {Elsevier},
Title = {Stimulators of translation identified during a small molecule screening campaign},
Volume = {447},
Year = {2014}}

A. J. Parks, M. P. Pollastri, M. E. Hahn, E. A. Stanford, O. Novikov, D. G. Franks, S. E. Haigh, S. Narasimhan, T. D. Ashton, T. G. Hopper, and others, “In silico identification of an aryl hydrocarbon receptor antagonist with biological activity in vitro and in vivo,” Molecular pharmacology, vol. 86, iss. 5, p. 593–608, 2014.
[BibTeX]

@article{parks2014silico,
Author = {Parks, Ashley J and Pollastri, Michael P and Hahn, Mark E and Stanford, Elizabeth A and Novikov, Olga and Franks, Diana G and Haigh, Sarah E and Narasimhan, Supraja and Ashton, Trent D and Hopper, Timothy G and others},
Journal = {Molecular pharmacology},
Number = {5},
Pages = {593--608},
Publisher = {American Society for Pharmacology and Experimental Therapeutics},
Title = {In silico identification of an aryl hydrocarbon receptor antagonist with biological activity in vitro and in vivo},
Volume = {86},
Year = {2014}}

2013

D. Kozakov, D. Beglov, T. Bohnuud, S. E. Mottarella, B. Xia, D. R. Hall, and S. Vajda, “How good is automated protein docking?,” Proteins: structure, function, and bioinformatics, vol. 81, iss. 12, p. 2159–2166, 2013.
[BibTeX]

@article{kozakov2013good,
Author = {Kozakov, Dima and Beglov, Dmitri and Bohnuud, Tanggis and Mottarella, Scott E and Xia, Bing and Hall, David R and Vajda, Sandor},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {12},
Pages = {2159--2166},
Title = {How good is automated protein docking?},
Volume = {81},
Year = {2013}}

R. Moretti, S. J. Fleishman, R. Agius, M. Torchala, P. A. Bates, P. L. Kastritis, J. P. Rodrigues, M. Trellet, A. M. Bonvin, M. Cui, and others, “Community-wide evaluation of methods for predicting the effect of mutations on protein–protein interactions,” Proteins: structure, function, and bioinformatics, vol. 81, iss. 11, p. 1980–1987, 2013.
[BibTeX]

@article{moretti2013community,
Author = {Moretti, Rocco and Fleishman, Sarel J and Agius, Rudi and Torchala, Mieczyslaw and Bates, Paul A and Kastritis, Panagiotis L and Rodrigues, Joao PGLM and Trellet, Mika{\"e}l and Bonvin, Alexandre MJJ and Cui, Meng and others},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {11},
Pages = {1980--1987},
Title = {Community-wide evaluation of methods for predicting the effect of mutations on protein--protein interactions},
Volume = {81},
Year = {2013}}

M. S. Golden, S. M. Cote, M. Sayeg, B. S. Zerbe, E. A. Villar, D. Beglov, S. L. Sazinsky, R. M. Georgiadis, S. Vajda, D. Kozakov, and others, “Comprehensive experimental and computational analysis of binding energy hot spots at the nf-$\kappa$b essential modulator/ikk$\beta$ protein–protein interface,” Journal of the american chemical society, vol. 135, iss. 16, p. 6242–6256, 2013.
[BibTeX]

@article{golden2013comprehensive,
Author = {Golden, Mary S and Cote, Shaun M and Sayeg, Marianna and Zerbe, Brandon S and Villar, Elizabeth A and Beglov, Dmitri and Sazinsky, Stephen L and Georgiadis, Rosina M and Vajda, Sandor and Kozakov, Dima and others},
Journal = {Journal of the American Chemical Society},
Number = {16},
Pages = {6242--6256},
Publisher = {American Chemical Society},
Title = {Comprehensive experimental and computational analysis of binding energy hot spots at the NF-$\kappa$B Essential Modulator/IKK$\beta$ protein--protein Interface},
Volume = {135},
Year = {2013}}

S. Vajda, D. R. Hall, and D. Kozakov, “Sampling and scoring: a marriage made in heaven,” Proteins: structure, function, and bioinformatics, vol. 81, iss. 11, p. 1874–1884, 2013.
[BibTeX]

@article{vajda2013sampling,
Author = {Vajda, Sandor and Hall, David R and Kozakov, Dima},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {11},
Pages = {1874--1884},
Title = {Sampling and scoring: A marriage made in heaven},
Volume = {81},
Year = {2013}}

A. Lavi, C. H. Ngan, D. Movshovitz-Attias, T. Bohnuud, C. Yueh, D. Beglov, O. Schueler-Furman, and D. Kozakov, “Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions,” Proteins: structure, function, and bioinformatics, vol. 81, iss. 12, p. 2096–2105, 2013.
[BibTeX]

@article{lavi2013detection,
Author = {Lavi, Assaf and Ngan, Chi Ho and Movshovitz-Attias, Dana and Bohnuud, Tanggis and Yueh, Christine and Beglov, Dmitri and Schueler-Furman, Ora and Kozakov, Dima},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {12},
Pages = {2096--2105},
Title = {Detection of peptide-binding sites on protein surfaces: The first step toward the modeling and targeting of peptide-mediated interactions},
Volume = {81},
Year = {2013}}

L. E. Grove, D. R. Hall, D. Beglov, S. Vajda, and D. Kozakov, “Ftflex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots,” Bioinformatics, vol. 29, iss. 9, p. 1218–1219, 2013.
[BibTeX]

@article{grove2013ftflex,
Author = {Grove, Laurie E and Hall, David R and Beglov, Dmitri and Vajda, Sandor and Kozakov, Dima},
Journal = {Bioinformatics},
Number = {9},
Pages = {1218--1219},
Publisher = {Oxford University Press},
Title = {FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots},
Volume = {29},
Year = {2013}}

M. Moghadasi, D. Kozakov, P. Vakili, S. Vajda, and I. C. Paschalidis, “A new distributed algorithm for side-chain positioning in the process of protein docking,” in 52nd ieee conference on decision and control, 2013, p. 739–744.
[BibTeX]

@inproceedings{moghadasi2013new,
Author = {Moghadasi, Mohammad and Kozakov, Dima and Vakili, Pirooz and Vajda, Sandor and Paschalidis, Ioannis Ch},
Booktitle = {52nd IEEE Conference on Decision and Control},
Organization = {IEEE},
Pages = {739--744},
Title = {A new distributed algorithm for side-chain positioning in the process of protein docking},
Year = {2013}}

H. Mirzaei, E. Villar, S. Mottarella, D. Beglov, I. C. Paschalidis, S. Vajda, D. Kozakov, and P. Vakili, “Flexible refinement of protein-ligand docking on manifolds,” in 52nd ieee conference on decision and control, 2013, p. 1392–1397.
[BibTeX]

@inproceedings{mirzaei2013flexible,
Author = {Mirzaei, Hanieh and Villar, Elizabeth and Mottarella, Scott and Beglov, Dmitri and Paschalidis, Ioannis Ch and Vajda, Sandor and Kozakov, Dima and Vakili, Pirooz},
Booktitle = {52nd IEEE Conference on Decision and Control},
Organization = {IEEE},
Pages = {1392--1397},
Title = {Flexible refinement of protein-ligand docking on manifolds},
Year = {2013}}

O. Kakhlon, H. Glickstein, N. Feinstein, H. Akman, S. DiMauro, B. Minassian, A. Michaeli, A. Rayan, T. Grossman, L. Solmesky, and others, Searching for efficient therapeutic avenues to treat adult polyglucosan body disease (apbd) and lafora disease (ld) using a high-throughput screening platform (p03. 053)Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology, 2013.
[BibTeX]

@misc{kakhlon2013searching,
Author = {Kakhlon, Or and Glickstein, Hava and Feinstein, Naomi and Akman, Hasan and DiMauro, Salvatore and Minassian, Berge and Michaeli, Amit and Rayan, Anwar and Grossman, Tamar and Solmesky, Leonardo and others},
Publisher = {Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology},
Title = {Searching for Efficient Therapeutic Avenues To Treat Adult Polyglucosan Body Disease (APBD) and Lafora Disease (LD) Using a High-Throughput Screening Platform (P03. 053)},
Year = {2013}}

2012

B. S. Zerbe, D. R. Hall, S. Vajda, A. Whitty, and D. Kozakov, “Relationship between hot spot residues and ligand binding hot spots in protein–protein interfaces,” Journal of chemical information and modeling, vol. 52, iss. 8, p. 2236–2244, 2012.
[BibTeX]

@article{zerbe2012relationship,
Author = {Zerbe, Brandon S and Hall, David R and Vajda, Sandor and Whitty, Adrian and Kozakov, Dima},
Journal = {Journal of chemical information and modeling},
Number = {8},
Pages = {2236--2244},
Publisher = {American Chemical Society},
Title = {Relationship between hot spot residues and ligand binding hot spots in protein--protein interfaces},
Volume = {52},
Year = {2012}}

C. H. Ngan, T. Bohnuud, S. E. Mottarella, D. Beglov, E. A. Villar, D. R. Hall, D. Kozakov, and S. Vajda, “Ftmap: extended protein mapping with user-selected probe molecules,” Nucleic acids research, vol. 40, iss. W1, p. W271–W275, 2012.
[BibTeX]

@article{ngan2012ftmap,
Author = {Ngan, Chi Ho and Bohnuud, Tanggis and Mottarella, Scott E and Beglov, Dmitri and Villar, Elizabeth A and Hall, David R and Kozakov, Dima and Vajda, Sandor},
Journal = {Nucleic acids research},
Number = {W1},
Pages = {W271--W275},
Publisher = {Oxford University Press},
Title = {FTMAP: extended protein mapping with user-selected probe molecules},
Volume = {40},
Year = {2012}}

R. Brenke, D. R. Hall, G. Chuang, S. R. Comeau, T. Bohnuud, D. Beglov, O. Schueler-Furman, S. Vajda, and D. Kozakov, “Application of asymmetric statistical potentials to antibody–protein docking,” Bioinformatics, vol. 28, iss. 20, p. 2608–2614, 2012.
[BibTeX]

@article{brenke2012application,
Author = {Brenke, Ryan and Hall, David R and Chuang, Gwo-Yu and Comeau, Stephen R and Bohnuud, Tanggis and Beglov, Dmitri and Schueler-Furman, Ora and Vajda, Sandor and Kozakov, Dima},
Journal = {Bioinformatics},
Number = {20},
Pages = {2608--2614},
Publisher = {Oxford University Press},
Title = {Application of asymmetric statistical potentials to antibody--protein docking},
Volume = {28},
Year = {2012}}

D. Beglov, D. R. Hall, R. Brenke, M. V. Shapovalov, R. L. Dunbrack Jr, D. Kozakov, and S. Vajda, “Minimal ensembles of side chain conformers for modeling protein–protein interactions,” Proteins: structure, function, and bioinformatics, vol. 80, iss. 2, p. 591–601, 2012.
[BibTeX]

@article{beglov2012minimal,
Author = {Beglov, Dmitri and Hall, David R and Brenke, Ryan and Shapovalov, Maxim V and Dunbrack Jr, Roland L and Kozakov, Dima and Vajda, Sandor},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {2},
Pages = {591--601},
Publisher = {Wiley Subscription Services, Inc., A Wiley Company Hoboken},
Title = {Minimal ensembles of side chain conformers for modeling protein--protein interactions},
Volume = {80},
Year = {2012}}

T. Bohnuud, D. Beglov, C. H. Ngan, B. Zerbe, D. R. Hall, R. Brenke, S. Vajda, M. D. Frank-Kamenetskii, and D. Kozakov, “Computational mapping reveals dramatic effect of hoogsteen breathing on duplex dna reactivity with formaldehyde,” Nucleic acids research, vol. 40, iss. 16, p. 7644–7652, 2012.
[BibTeX]

@article{bohnuud2012computational,
Author = {Bohnuud, Tanggis and Beglov, Dmitri and Ngan, Chi Ho and Zerbe, Brandon and Hall, David R and Brenke, Ryan and Vajda, Sandor and Frank-Kamenetskii, Maxim D and Kozakov, Dima},
Journal = {Nucleic acids research},
Number = {16},
Pages = {7644--7652},
Publisher = {Oxford University Press},
Title = {Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde},
Volume = {40},
Year = {2012}}

H. Mirzaei, D. Beglov, I. C. Paschalidis, S. Vajda, P. Vakili, and D. Kozakov, “Rigid body energy minimization on manifolds for molecular docking,” Journal of chemical theory and computation, vol. 8, iss. 11, p. 4374–4380, 2012.
[BibTeX]

@article{mirzaei2012rigid,
Author = {Mirzaei, Hanieh and Beglov, Dmitri and Paschalidis, Ioannis Ch and Vajda, Sandor and Vakili, Pirooz and Kozakov, Dima},
Journal = {Journal of chemical theory and computation},
Number = {11},
Pages = {4374--4380},
Publisher = {American Chemical Society},
Title = {Rigid body energy minimization on manifolds for molecular docking},
Volume = {8},
Year = {2012}}

S. Hingtgen, R. Kasmieh, E. Elbayly, I. Nesterenko, J. Figueiredo, R. Dash, D. Sarkar, D. Hall, D. Kozakov, S. Vajda, and others, “A first-generation multi-functional cytokine for simultaneous optical tracking and tumor therapy,” Plos one, vol. 7, iss. 7, p. e40234, 2012.
[BibTeX]

@article{hingtgen2012first,
Author = {Hingtgen, Shawn and Kasmieh, Randa and Elbayly, Elizabeth and Nesterenko, Irina and Figueiredo, Jose-Luiz and Dash, Rupesh and Sarkar, Devanand and Hall, David and Kozakov, Dima and Vajda, Sandor and others},
Journal = {PloS one},
Number = {7},
Pages = {e40234},
Publisher = {Public Library of Science},
Title = {A first-generation multi-functional cytokine for simultaneous optical tracking and tumor therapy},
Volume = {7},
Year = {2012}}

D. R. Hall, D. Kozakov, and S. Vajda, “Analysis of protein binding sites by computational solvent mapping,” in Computational drug discovery and design, Springer, New York, NY, 2012, p. 13–27.
[BibTeX]

@incollection{hall2012analysis,
Author = {Hall, David R and Kozakov, Dima and Vajda, Sandor},
Booktitle = {Computational drug discovery and design},
Pages = {13--27},
Publisher = {Springer, New York, NY},
Title = {Analysis of protein binding sites by computational solvent mapping},
Year = {2012}}

H. Mirzaei, D. Kozakov, D. Beglov, I. C. Paschalidis, S. Vajda, and P. Vakili, “A new approach to rigid body minimization with application to molecular docking,” in 2012 ieee 51st ieee conference on decision and control (cdc), 2012, p. 2983–2988.
[BibTeX]

@inproceedings{mirzaei2012new,
Author = {Mirzaei, Hanieh and Kozakov, Dima and Beglov, Dmitri and Paschalidis, Ioannis Ch and Vajda, Sandor and Vakili, Pirooz},
Booktitle = {2012 IEEE 51st IEEE Conference on Decision and Control (CDC)},
Organization = {IEEE},
Pages = {2983--2988},
Title = {A new approach to rigid body minimization with application to molecular docking},
Year = {2012}}

M. Moghadasi, D. Kozakov, A. B. Mamonov, P. Vakili, S. Vajda, and I. C. Paschalidis, “A message passing approach to side chain positioning with applications in protein docking refinement,” in 2012 ieee 51st ieee conference on decision and control (cdc), 2012, p. 2310–2315.
[BibTeX]

@inproceedings{moghadasi2012message,
Author = {Moghadasi, Mohammad and Kozakov, Dima and Mamonov, Artem B and Vakili, Pirooz and Vajda, Sandor and Paschalidis, Ioannis Ch},
Booktitle = {2012 IEEE 51st IEEE Conference on Decision and Control (CDC)},
Organization = {IEEE},
Pages = {2310--2315},
Title = {A message passing approach to side chain positioning with applications in protein docking refinement},
Year = {2012}}

2011

D. Kozakov, D. R. Hall, G. Chuang, R. Cencic, R. Brenke, L. E. Grove, D. Beglov, J. Pelletier, A. Whitty, and S. Vajda, “Structural conservation of druggable hot spots in protein–protein interfaces,” Proceedings of the national academy of sciences, vol. 108, iss. 33, p. 13528–13533, 2011.
[BibTeX]

@article{kozakov2011structural,
Author = {Kozakov, Dima and Hall, David R and Chuang, Gwo-Yu and Cencic, Regina and Brenke, Ryan and Grove, Laurie E and Beglov, Dmitri and Pelletier, Jerry and Whitty, Adrian and Vajda, Sandor},
Journal = {Proceedings of the National Academy of Sciences},
Number = {33},
Pages = {13528--13533},
Publisher = {National Academy of Sciences},
Title = {Structural conservation of druggable hot spots in protein--protein interfaces},
Volume = {108},
Year = {2011}}

R. Cencic, D. R. Hall, F. Robert, Y. Du, J. Min, L. Li, M. Qui, I. Lewis, S. Kurtkaya, R. Dingledine, and others, “Reversing chemoresistance by small molecule inhibition of the translation initiation complex eif4f,” Proceedings of the national academy of sciences, vol. 108, iss. 3, p. 1046–1051, 2011.
[BibTeX]

@article{cencic2011reversing,
Author = {Cencic, Regina and Hall, David R and Robert, Francis and Du, Yuhong and Min, Jaeki and Li, Lian and Qui, Min and Lewis, Iestyn and Kurtkaya, Serdar and Dingledine, Ray and others},
Journal = {Proceedings of the National Academy of Sciences},
Number = {3},
Pages = {1046--1051},
Publisher = {National Academy of Sciences},
Title = {Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F},
Volume = {108},
Year = {2011}}

G. Buhrman, O. Casey, B. Zerbe, B. M. Kearney, R. Napoleon, E. A. Kovrigina, S. Vajda, D. Kozakov, E. L. Kovrigin, C. Mattos, and others, “Analysis of binding site hot spots on the surface of ras gtpase,” Journal of molecular biology, vol. 413, iss. 4, p. 773–789, 2011.
[BibTeX]

@article{buhrman2011analysis,
Author = {Buhrman, Greg and Casey, O and Zerbe, Brandon and Kearney, Bradley M and Napoleon, Raeanne and Kovrigina, Elizaveta A and Vajda, Sandor and Kozakov, Dima and Kovrigin, Evgenii L and Mattos, Carla and others},
Journal = {Journal of molecular biology},
Number = {4},
Pages = {773--789},
Publisher = {Elsevier},
Title = {Analysis of binding site hot spots on the surface of Ras GTPase},
Volume = {413},
Year = {2011}}

C. Ngan, D. R. Hall, B. Zerbe, L. E. Grove, D. Kozakov, and S. Vajda, “Ftsite: high accuracy detection of ligand binding sites on unbound protein structures,” Bioinformatics, vol. 28, iss. 2, p. 286–287, 2011.
[BibTeX]

@article{ngan2011ftsite,
Author = {Ngan, Chi-Ho and Hall, David R and Zerbe, Brandon and Grove, Laurie E and Kozakov, Dima and Vajda, Sandor},
Journal = {Bioinformatics},
Number = {2},
Pages = {286--287},
Publisher = {Oxford University Press},
Title = {FTSite: high accuracy detection of ligand binding sites on unbound protein structures},
Volume = {28},
Year = {2011}}

R. Cencic, M. Desforges, D. R. Hall, D. Kozakov, Y. Du, J. Min, R. Dingledine, H. Fu, S. Vajda, P. J. Talbot, and others, “Blocking eif4e-eif4g interaction as a strategy to impair coronavirus replication,” Journal of virology, vol. 85, iss. 13, p. 6381–6389, 2011.
[BibTeX]

@article{cencic2011blocking,
Author = {Cencic, Regina and Desforges, Marc and Hall, David R and Kozakov, Dima and Du, Yuhong and Min, Jaeki and Dingledine, Raymond and Fu, Haian and Vajda, Sandor and Talbot, Pierre J and others},
Journal = {Journal of virology},
Number = {13},
Pages = {6381--6389},
Publisher = {American Society for Microbiology Journals},
Title = {Blocking eIF4E-eIF4G interaction as a strategy to impair coronavirus replication},
Volume = {85},
Year = {2011}}

D. R. Hall, C. H. Ngan, B. S. Zerbe, D. Kozakov, and S. Vajda, “Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery,” Journal of chemical information and modeling, vol. 52, iss. 1, p. 199–209, 2011.
[BibTeX]

@article{hall2011hot,
Author = {Hall, David R and Ngan, Chi Ho and Zerbe, Brandon S and Kozakov, Dima and Vajda, Sandor},
Journal = {Journal of chemical information and modeling},
Number = {1},
Pages = {199--209},
Publisher = {American Chemical Society},
Title = {Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery},
Volume = {52},
Year = {2011}}

G. V. Callard, A. M. Tarrant, A. Novillo, P. Yacci, L. Ciaccia, S. Vajda, G-Y. Chuang, D. Kozakov, S. Greytak, S. Sawyer, and others, “Evolutionary origins of the estrogen signaling system: insights from amphioxus,” The journal of steroid biochemistry and molecular biology, vol. 127, iss. 3-5, p. 176–188, 2011.
[BibTeX]

@article{callard2011evolutionary,
Author = {Callard, Gloria V and Tarrant, Ann M and Novillo, A and Yacci, P and Ciaccia, L and Vajda, S and Chuang, G-Y and Kozakov, D and Greytak, SR and Sawyer, S and others},
Journal = {The Journal of steroid biochemistry and molecular biology},
Number = {3-5},
Pages = {176--188},
Publisher = {Pergamon},
Title = {Evolutionary origins of the estrogen signaling system: insights from amphioxus},
Volume = {127},
Year = {2011}}

D. H. Hall, L. E. Grove, C. Yueh, C. H. Ngan, D. Kozakov, and S. Vajda, “Robust identification of binding hot spots using continuum electrostatics: application to hen egg-white lysozyme,” Journal of the american chemical society, vol. 133, iss. 51, p. 20668–20671, 2011.
[BibTeX]

@article{hall2011robust,
Author = {Hall, David H and Grove, Laurie E and Yueh, Christine and Ngan, Chi Ho and Kozakov, Dima and Vajda, Sandor},
Journal = {Journal of the American Chemical Society},
Number = {51},
Pages = {20668--20671},
Publisher = {American Chemical Society},
Title = {Robust identification of binding hot spots using continuum electrostatics: application to hen egg-white lysozyme},
Volume = {133},
Year = {2011}}

2010

D. Kozakov, D. R. Hall, D. Beglov, R. Brenke, S. R. Comeau, Y. Shen, K. Li, J. Zheng, P. Vakili, I. C. Paschalidis, and others, “Achieving reliability and high accuracy in automated protein docking: cluspro, piper, sdu, and stability analysis in capri rounds 13–19,” Proteins: structure, function, and bioinformatics, vol. 78, iss. 15, p. 3124–3130, 2010.
[BibTeX]

@article{kozakov2010achieving,
Author = {Kozakov, Dima and Hall, David R and Beglov, Dmitri and Brenke, Ryan and Comeau, Stephen R and Shen, Yang and Li, Keyong and Zheng, Jiefu and Vakili, Pirooz and Paschalidis, Ioannis Ch and others},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {15},
Pages = {3124--3130},
Publisher = {Wiley Online Library},
Title = {Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13--19},
Volume = {78},
Year = {2010}}

D. Kozakov, G. Chuang, D. Beglov, and S. Vajda, “Where does amantadine bind to the influenza virus m2 proton channel?,” Trends in biochemical sciences, vol. 35, iss. 9, p. 471–475, 2010.
[BibTeX]

@article{kozakov2010does,
Author = {Kozakov, Dima and Chuang, Gwo-Yu and Beglov, Dmitri and Vajda, Sandor},
Journal = {Trends in biochemical sciences},
Number = {9},
Pages = {471--475},
Publisher = {Elsevier Current Trends},
Title = {Where does amantadine bind to the influenza virus M2 proton channel?},
Volume = {35},
Year = {2010}}

G. Chuang, R. Mehra-Chaudhary, C. Ngan, B. S. Zerbe, D. Kozakov, S. Vajda, and L. J. Beamer, “Domain motion and interdomain hot spots in a multidomain enzyme,” Protein science, vol. 19, iss. 9, p. 1662–1672, 2010.
[BibTeX]

@article{chuang2010domain,
Author = {Chuang, Gwo-Yu and Mehra-Chaudhary, Ritcha and Ngan, Chi-Ho and Zerbe, Brandon S and Kozakov, Dima and Vajda, Sandor and Beamer, Lesa J},
Journal = {Protein Science},
Number = {9},
Pages = {1662--1672},
Publisher = {Wiley Subscription Services, Inc., A Wiley Company Hoboken},
Title = {Domain motion and interdomain hot spots in a multidomain enzyme},
Volume = {19},
Year = {2010}}

2009

R. Brenke, D. Kozakov, G. Chuang, D. Beglov, D. Hall, M. R. Landon, C. Mattos, and S. Vajda, “Fragment-based identification of druggable `hot spots’ of proteins using fourier domain correlation techniques,” Bioinformatics, vol. 25, iss. 5, p. 621–627, 2009.
[BibTeX]

@article{brenke2009fragment,
Author = {Brenke, Ryan and Kozakov, Dima and Chuang, Gwo-Yu and Beglov, Dmitri and Hall, David and Landon, Melissa R and Mattos, Carla and Vajda, Sandor},
Journal = {Bioinformatics},
Number = {5},
Pages = {621--627},
Publisher = {Oxford University Press},
Title = {Fragment-based identification of druggable `hot spots' of proteins using Fourier domain correlation techniques},
Volume = {25},
Year = {2009}}

S. Vajda and D. Kozakov, “Convergence and combination of methods in protein–protein docking,” Current opinion in structural biology, vol. 19, iss. 2, p. 164–170, 2009.
[BibTeX]

@article{vajda2009convergence,
Author = {Vajda, Sandor and Kozakov, Dima},
Journal = {Current opinion in structural biology},
Number = {2},
Pages = {164--170},
Publisher = {Elsevier Current Trends},
Title = {Convergence and combination of methods in protein--protein docking},
Volume = {19},
Year = {2009}}

M. R. Landon, R. L. Lieberman, Q. Q. Hoang, S. Ju, J. M. Caaveiro, S. D. Orwig, D. Kozakov, R. Brenke, G. Chuang, D. Beglov, and others, “Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to dj-1 and glucocerebrosidase,” Journal of computer-aided molecular design, vol. 23, iss. 8, p. 491–500, 2009.
[BibTeX]

@article{landon2009detection,
Author = {Landon, Melissa R and Lieberman, Raquel L and Hoang, Quyen Q and Ju, Shulin and Caaveiro, Jose MM and Orwig, Susan D and Kozakov, Dima and Brenke, Ryan and Chuang, Gwo-Yu and Beglov, Dmitry and others},
Journal = {Journal of computer-aided molecular design},
Number = {8},
Pages = {491--500},
Publisher = {Springer},
Title = {Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase},
Volume = {23},
Year = {2009}}

C. Ngan, D. Beglov, A. N. Rudnitskaya, D. Kozakov, D. J. Waxman, and S. Vajda, “The structural basis of pregnane x receptor binding promiscuity,” Biochemistry, vol. 48, iss. 48, p. 11572–11581, 2009.
[BibTeX]

@article{ngan2009structural,
Author = {Ngan, Chi-Ho and Beglov, Dmitri and Rudnitskaya, Aleksandra N and Kozakov, Dima and Waxman, David J and Vajda, Sandor},
Journal = {Biochemistry},
Number = {48},
Pages = {11572--11581},
Publisher = {American Chemical Society},
Title = {The structural basis of pregnane X receptor binding promiscuity},
Volume = {48},
Year = {2009}}

G. Chuang, D. Kozakov, R. Brenke, D. Beglov, F. Guarnieri, and S. Vajda, “Binding hot spots and amantadine orientation in the influenza a virus m2 proton channel,” Biophysical journal, vol. 97, iss. 10, p. 2846–2853, 2009.
[BibTeX]

@article{chuang2009binding,
Author = {Chuang, Gwo-Yu and Kozakov, Dima and Brenke, Ryan and Beglov, Dmitri and Guarnieri, Frank and Vajda, Sandor},
Journal = {Biophysical journal},
Number = {10},
Pages = {2846--2853},
Publisher = {Elsevier},
Title = {Binding hot spots and amantadine orientation in the influenza a virus M2 proton channel},
Volume = {97},
Year = {2009}}

D. Beglov, C. Lee, A. De Biasio, D. Kozakov, R. Brenke, S. Vajda, and N. Beglova, “Structural insights into recognition of $\beta$2-glycoprotein i by the lipoprotein receptors,” Proteins: structure, function, and bioinformatics, vol. 77, iss. 4, p. 940–949, 2009.
[BibTeX]

@article{beglov2009structural,
Author = {Beglov, Dmitri and Lee, Chang-Jin and De Biasio, Alfredo and Kozakov, Dima and Brenke, Ryan and Vajda, Sandor and Beglova, Natalia},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {4},
Pages = {940--949},
Publisher = {Wiley Subscription Services, Inc., A Wiley Company Hoboken},
Title = {Structural insights into recognition of $\beta$2-glycoprotein I by the lipoprotein receptors},
Volume = {77},
Year = {2009}}

D. Beglov, R. Brenke, G. Chuang, D. Hall, M. Landon, C. H. Ngan, Y. Shen, S. Thiel, B. Zerbe, D. Kozakov, and others, “13 identification of druggable hot spots on proteins and in protein–protein interfaces,” Computational protein-protein interactions, p. 253, 2009.
[BibTeX]

@article{beglov200913,
Author = {Beglov, Dmitri and Brenke, Ryan and Chuang, Gwo-Yu and Hall, David and Landon, Melissa and Ngan, Chi Ho and Shen, Yang and Thiel, Spencer and Zerbe, Brandon and Kozakov, Dima and others},
Journal = {Computational Protein-Protein Interactions},
Pages = {253},
Publisher = {CRC Press},
Title = {13 Identification of Druggable Hot Spots on Proteins and in Protein--Protein Interfaces},
Year = {2009}}

J. Janin, “Basic principles of protein–protein interaction,” Computational protein–protein interactions, p. 1–20, 2009.
[BibTeX]

@article{janin2009basic,
Author = {Janin, Jo{\"e}l},
Journal = {Computational protein--protein interactions},
Pages = {1--20},
Publisher = {Taylor \& Francis Group New York, NY},
Title = {Basic principles of protein--protein interaction},
Year = {2009}}

2008

D. W. Ritchie, D. Kozakov, and S. Vajda, “Accelerating and focusing protein–protein docking correlations using multi-dimensional rotational fft generating functions,” Bioinformatics, vol. 24, iss. 17, p. 1865–1873, 2008.
[BibTeX]

@article{ritchie2008accelerating,
Author = {Ritchie, David W and Kozakov, Dima and Vajda, Sandor},
Journal = {Bioinformatics},
Number = {17},
Pages = {1865--1873},
Publisher = {Oxford University Press},
Title = {Accelerating and focusing protein--protein docking correlations using multi-dimensional rotational FFT generating functions},
Volume = {24},
Year = {2008}}

G. Chuang, D. Kozakov, R. Brenke, S. R. Comeau, and S. Vajda, “Dars (decoys as the reference state) potentials for protein-protein docking,” Biophysical journal, vol. 95, iss. 9, p. 4217–4227, 2008.
[BibTeX]

@article{chuang2008dars,
Author = {Chuang, Gwo-Yu and Kozakov, Dima and Brenke, Ryan and Comeau, Stephen R and Vajda, Sandor},
Journal = {Biophysical journal},
Number = {9},
Pages = {4217--4227},
Publisher = {Elsevier},
Title = {DARS (Decoys As the Reference State) potentials for protein-protein docking},
Volume = {95},
Year = {2008}}

D. Kozakov, O. Schueler-Furman, and S. Vajda, “Discrimination of near-native structures in protein–protein docking by testing the stability of local minima,” Proteins: structure, function, and bioinformatics, vol. 72, iss. 3, p. 993–1004, 2008.
[BibTeX]

@article{kozakov2008discrimination,
Author = {Kozakov, Dima and Schueler-Furman, Ora and Vajda, Sandor},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {3},
Pages = {993--1004},
Publisher = {Wiley Online Library},
Title = {Discrimination of near-native structures in protein--protein docking by testing the stability of local minima},
Volume = {72},
Year = {2008}}

2007

S. R. Comeau, D. Kozakov, R. Brenke, Y. Shen, D. Beglov, and S. Vajda, “Cluspro: performance in capri rounds 6–11 and the new server,” Proteins: structure, function, and bioinformatics, vol. 69, iss. 4, p. 781–785, 2007.
[BibTeX]

@article{comeau2007cluspro,
Author = {Comeau, Stephen R and Kozakov, Dima and Brenke, Ryan and Shen, Yang and Beglov, Dmitri and Vajda, Sandor},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {4},
Pages = {781--785},
Publisher = {Wiley Subscription Services, Inc., A Wiley Company Hoboken},
Title = {ClusPro: performance in CAPRI rounds 6--11 and the new server},
Volume = {69},
Year = {2007}}

Y. Shen, R. Brenke, D. Kozakov, S. R. Comeau, D. Beglov, and S. Vajda, “Docking with piper and refinement with sdu in rounds 6–11 of capri,” Proteins: structure, function, and bioinformatics, vol. 69, iss. 4, p. 734–742, 2007.
[BibTeX]

@article{shen2007docking,
Author = {Shen, Yang and Brenke, Ryan and Kozakov, Dima and Comeau, Stephen R and Beglov, Dmitri and Vajda, Sandor},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {4},
Pages = {734--742},
Publisher = {Wiley-Blackwell},
Title = {Docking with PIPER and refinement with SDU in rounds 6--11 of CAPRI},
Volume = {69},
Year = {2007}}

2006

D. Kozakov, R. Brenke, S. R. Comeau, and S. Vajda, “Piper: an fft-based protein docking program with pairwise potentials,” Proteins: structure, function, and bioinformatics, vol. 65, iss. 2, p. 392–406, 2006.
[BibTeX]

@article{kozakov2006piper,
Author = {Kozakov, Dima and Brenke, Ryan and Comeau, Stephen R and Vajda, Sandor},
Journal = {Proteins: Structure, Function, and Bioinformatics},
Number = {2},
Pages = {392--406},
Publisher = {Wiley Online Library},
Title = {PIPER: an FFT-based protein docking program with pairwise potentials},
Volume = {65},
Year = {2006}}

S. Vajda, D. Kozakov, R. Brenke, S. Comeau, Y. Shen, P. Vakili, and I. C. Paschalidis, “Biot 194-new approaches to protein-protein docking,” in Abstracts of papers of the american chemical society, 2006.
[BibTeX]

@inproceedings{vajda2006biot,
Author = {Vajda, Sandor and Kozakov, Dima and Brenke, Ryan and Comeau, Stephen and Shen, Yang and Vakili, Pirooz and Paschalidis, Ioannis Ch},
Booktitle = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
Organization = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Title = {BIOT 194-New approaches to protein-protein docking},
Volume = {232},
Year = {2006}}

2005

D. Kozakov, K. H. Clodfelter, S. Vajda, and C. J. Camacho, “Optimal clustering for detecting near-native conformations in protein docking,” Biophysical journal, vol. 89, iss. 2, p. 867–875, 2005.
[BibTeX]

@article{kozakov2005optimal,
Author = {Kozakov, Dima and Clodfelter, Karl H and Vajda, Sandor and Camacho, Carlos J},
Journal = {Biophysical journal},
Number = {2},
Pages = {867--875},
Publisher = {Cell Press},
Title = {Optimal clustering for detecting near-native conformations in protein docking},
Volume = {89},
Year = {2005}}