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, title={ClusPro LigTBM: Automated template-based small molecule docking}, 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}, volume={432}, number={11}, pages={3404--3410}, year={2020}, publisher={Academic Press} } - 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, title={Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45}, 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}, volume={88}, number={8}, pages={1037--1049}, year={2020}, publisher={John Wiley \& Sons, Inc. Hoboken, USA} } - 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, title={Performance and Its Limits in Rigid Body Protein-Protein Docking}, author={Desta, Israel T and Porter, Kathryn A and Xia, Bing and Kozakov, Dima and Vajda, Sandor}, journal={Structure}, volume={28}, number={9}, pages={1071--1081}, year={2020}, publisher={Cell Press} } - 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, title={ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking}, 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}, journal={Proteins: Structure, Function, and Bioinformatics}, volume={88}, number={8}, pages={1082--1090}, year={2020}, publisher={John Wiley \& Sons, Inc. Hoboken, USA} } - 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. 80, iss. 6, p. 1104–1122, 2020.
[BibTeX]@article{hekman2020actionable, title={Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2}, 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 Bree and Suder, Ellen L and Paul, Indranil and Phanse, Sadhna and others}, journal={Molecular cell}, volume={80}, number={6}, pages={1104--1122}, year={2020}, publisher={Cell Press} } - A. E. Wakefield, C. Yueh, D. Beglov, M. S. Castilho, D. Kozakov, G. M. Keserű, A. Whitty, and S. Vajda, “Benchmark sets for binding hot spot identification in fragment-based ligand discovery,” Journal of chemical information and modeling, 2020.
[BibTeX]@article{wakefield2020benchmark, title={Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery}, author={Wakefield, Amanda E and Yueh, Christine and Beglov, Dmitri and Castilho, Marcelo S and Kozakov, Dima and Keserű, György M and Whitty, Adrian and Vajda, Sandor}, journal={Journal of Chemical Information and Modeling}, year={2020}, publisher={American Chemical Society} }
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, iss. 1, p. 119–127, 2019.
[BibTeX]@article{ignatov2019monte, title={Monte Carlo on the manifold and MD refinement for binding pose prediction of protein--ligand complexes: 2017 D3R Grand Challenge}, 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}, journal={Journal of computer-aided molecular design}, volume={33}, number={1}, pages={119--127}, year={2019}, publisher={Springer International Publishing} } - 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, title={What method to use for protein--protein docking?}, author={Porter, Kathryn A and Desta, Israel and Kozakov, Dima and Vajda, Sandor}, journal={Current opinion in structural biology}, volume={55}, pages={1--7}, year={2019}, publisher={Elsevier Current Trends} } - 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, 2019.
[BibTeX]@article{wodak2019allostery, title={Allostery in its many disguises: from theory to applications}, 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}, journal={Structure}, year={2019}, publisher={Cell Press} } - 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, title={Predicting Protein Dimer Structures Using MELD$\times$ MD}, author={Brini, Emiliano and Kozakov, Dima and Dill, Ken A}, journal={Journal of chemical theory and computation}, volume={15}, number={5}, pages={3381--3389}, year={2019}, publisher={American Chemical Society} } - C. Yueh, T. J. Rettenmaier, B. Xia, D. R. Hall, A. Alekseenko, K. A. Porter, K. Barkovich, G. M. Keseru, A. Whitty, J. A. Wells, and others, “Kinase atlas: druggability analysis of potential allosteric sites in kinases,” Journal of medicinal chemistry, 2019.
[BibTeX]@article{yueh2019kinase, title={Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases}, author={Yueh, Christine and Rettenmaier, Terry Justin and Xia, Bing and Hall, David R and Alekseenko, Andrey and Porter, Kathryn A and Barkovich, Krister and Keseru, Gyorgy M and Whitty, Adrian and Wells, James A and others}, journal={Journal of Medicinal Chemistry}, year={2019}, publisher={American Chemical Society} } - 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, 2019.
[BibTeX]@article{porter2019template, title={Template-Based Modeling by ClusPro in CASP13 and the Potential for Using Co-evolutionary Information in Docking}, 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}, journal={Proteins: Structure, Function, and Bioinformatics}, year={2019}, publisher={John Wiley \& Sons, Ltd} } - 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, title={Improved Modeling of Peptide-Protein Binding through Global Docking and Accelerated Molecular Dynamics Simulations}, author={Wang, Jinan and Alekseenko, Andrey and Kozakov, Dima and Miao, Yinglong}, journal={Frontiers in molecular biosciences}, volume={6}, pages={112}, year={2019}, publisher={Frontiers} } - 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, 2019.
[BibTeX]@article{lensink2019blind, title={Blind prediction of homo-and hetero-protein complexes: The CASP13-CAPRI experiment}, 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}, journal={Proteins: Structure, Function, and Bioinformatics}, year={2019}, publisher={John Wiley \& Sons, Ltd} } - 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, 2019.
[BibTeX]@article{alekseenko2019cluspro, title={ClusPro LigTBM: Automated Template-Based Small Molecule Docking}, 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}, year={2019}, publisher={Academic Press} } - M. Zhong, A. J. 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, 2019.
[BibTeX]@article{zhong2019interaction, 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)}, author={Zhong, Mengqi and Lynch, Andrew John 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}, journal={Biochemistry}, year={2019}, publisher={American Chemical Society} } - 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, p. 1–11, 2019.
[BibTeX]@article{kotelnikov2019sampling, title={Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4}, 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}, year={2019}, publisher={Springer International Publishing} }
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, iss. 1, p. 225–230, 2018.
[BibTeX]@article{padhorny2018protein, title={Protein--ligand docking using FFT based sampling: D3R case study}, 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}, journal={Journal of computer-aided molecular design}, volume={32}, number={1}, pages={225--230}, year={2018}, publisher={Springer International Publishing} } - 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, title={Exploring the structural origins of cryptic sites on proteins}, 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}, journal={Proceedings of the National Academy of Sciences}, volume={115}, number={15}, pages={E3416--E3425}, year={2018}, publisher={National Academy of Sciences} } - 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, title={ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking}, author={Ignatov, Mikhail and Kazennov, Andrey and Kozakov, Dima}, journal={Journal of molecular biology}, volume={430}, number={15}, pages={2249--2255}, year={2018}, publisher={Academic Press} } - 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, title={Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes}, 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}, journal={Scientific reports}, volume={8}, number={1}, pages={5896}, year={2018}, publisher={Nature Publishing Group} } - 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, title={Glucose regulation in the methylotrophic yeast Hansenula (Ogataea) polymorpha is mediated by a putative transceptor Gcr1}, 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}, volume={103}, pages={25--34}, year={2018}, publisher={Pergamon} }
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, title={A benchmark testing ground for integrating homology modeling and protein docking}, 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}, journal={Proteins: Structure, Function, and Bioinformatics}, volume={85}, number={1}, pages={10--16}, 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, title={ClusPro-DC: Dimer classification by the CLUSPRO server for protein--protein docking}, author={Yueh, Christine and Hall, David R and Xia, Bing and Padhorny, Dzmitry and Kozakov, Dima and Vajda, Sandor}, journal={Journal of molecular biology}, volume={429}, number={3}, pages={372--381}, year={2017}, publisher={Academic Press} } - 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, title={New additions to the C lus P ro server motivated by CAPRI}, 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}, journal={Proteins: Structure, Function, and Bioinformatics}, volume={85}, number={3}, pages={435--444}, 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, title={FlexPepDock lessons from CAPRI peptide--protein rounds and suggested new criteria for assessment of model quality and utility}, author={Marcu, Orly and Dodson, Emma-Joy and Alam, Nawsad and Sperber, Michal and Kozakov, Dima and Lensink, Marc F and Schueler-Furman, Ora}, journal={Proteins: Structure, Function, and Bioinformatics}, volume={85}, number={3}, pages={445--462}, 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, 2017.
[BibTeX]@article{kozakov2017cluspro, title={The ClusPro web server for protein--protein docking}, 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}, journal={Nature protocols}, volume={12}, number={2}, pages={255}, year={2017}, publisher={Nature Publishing Group} } - T. Bohnuud, G. Jones, O. Schueler-Furman, and D. Kozakov, “Detection of peptide-binding sites on protein surfaces using the peptimap server,” in Modeling peptide-protein interactions, Humana Press, New York, NY, 2017, p. 11–20.
[BibTeX]@incollection{bohnuud2017detection, title={Detection of peptide-binding sites on protein surfaces using the Peptimap server}, author={Bohnuud, Tanggis and Jones, George and Schueler-Furman, Ora and Kozakov, Dima}, booktitle={Modeling Peptide-Protein Interactions}, pages={11--20}, year={2017}, publisher={Humana Press, New York, NY} } - 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, title={ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT}, author={Porter, Kathryn A and Xia, Bing and Beglov, Dmitri and Bohnuud, Tanggis and Alam, Nawsad and Schueler-Furman, Ora and Kozakov, Dima}, journal={Bioinformatics}, volume={33}, number={20}, pages={3299--3301}, year={2017}, publisher={Oxford University Press} } - N. Alam, O. Goldstein, B. Xia, K. A. Porter, D. Kozakov, and O. Schueler-Furman, “High-resolution global peptide-protein docking using fragments-based piper-flexpepdock,” Plos computational biology, vol. 13, iss. 12, p. e1005905, 2017.
[BibTeX]@article{alam2017high, title={High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock}, author={Alam, Nawsad and Goldstein, Oriel and Xia, Bing and Porter, Kathryn A and Kozakov, Dima and Schueler-Furman, Ora}, journal={PLoS computational biology}, volume={13}, number={12}, pages={e1005905}, year={2017}, publisher={Public Library of Science} } - 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, title={High-resolution modeling of peptide-protein interactions using a fragment-based global docking approach, PIPER-FlexPepDock}, author={Alam, N and Kozakov, D and Schueler-Furman, O}, booktitle={Febs Journal}, volume={284}, pages={317--317}, year={2017}, organization={WILEY 111 RIVER ST, HOBOKEN 07030-5774, NJ USA} }
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, title={Focused grid-based resampling for protein docking and mapping}, 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}, journal={Journal of computational chemistry}, volume={37}, number={11}, pages={961--970}, 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, title={Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment}, 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}, journal={Proteins: Structure, Function, and Bioinformatics}, volume={84}, pages={323--348}, 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, title={Accounting for pairwise distance restraints in FFT-based protein--protein docking}, author={Xia, Bing and Vajda, Sandor and Kozakov, Dima}, journal={Bioinformatics}, volume={32}, number={21}, pages={3342--3344}, year={2016}, publisher={Oxford University Press} } - 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, title={Protein--protein docking by fast generalized Fourier transforms on 5D rotational manifolds}, 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}, journal={Proceedings of the National Academy of Sciences}, volume={113}, number={30}, pages={E4286--E4293}, year={2016}, publisher={National Academy of Sciences} } - L. E. Grove, S. Vajda, and D. Kozakov, Computational methods to support fragment-based drug discoveryWiley-VCH Verlag GmbH & Co. KGaA: Weinheim, Germany, 2016.
[BibTeX]@misc{grove2016computational, title={Computational methods to support fragment-based drug discovery}, author={Grove, Laurie E and Vajda, Sandor and Kozakov, Dima}, journal={Fragment-Based Drug Discovery Lessons and Outlook}, pages={197--222}, year={2016}, publisher={Wiley-VCH Verlag GmbH \& Co. KGaA: Weinheim, Germany} }
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, 2015.
[BibTeX]@article{kozakov2015ftmap, title={The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins}, 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}, journal={Nature protocols}, volume={10}, number={5}, pages={733}, year={2015}, publisher={Nature Publishing Group} } - 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, title={Ligand deconstruction: Why some fragment binding positions are conserved and others are not}, 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}, journal={Proceedings of the National Academy of Sciences}, volume={112}, number={20}, pages={E2585--E2594}, year={2015}, publisher={National Academy of Sciences} } - 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,” Journal of computational chemistry, vol. 36, iss. 20, p. 1568–1572, 2015.
[BibTeX]@article{xia2015accounting, title={Accounting for observed small angle X-ray scattering profile in the protein--protein docking server cluspro}, 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}, journal={Journal of computational chemistry}, volume={36}, number={20}, pages={1568--1572}, year={2015}, publisher={Wiley Online Library} } - 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, iss. 1_supplement, p. 712–20, 2015.
[BibTeX]@article{zhong2015fragment, title={Fragment-based drug discovery targeting KEAP1/Nrf2 binding}, author={Zhong, Mengqi and Lynch, Andrew and Jehle, Stefan and Kozakov, Dima and Vajda, Sandor and Allen, Karen and Whitty, Adrian}, journal={The FASEB Journal}, volume={29}, number={1\_supplement}, pages={712--20}, year={2015}, publisher={The Federation of American Societies for Experimental Biology} } - 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, title={Energy minimization on manifolds for docking flexible molecules}, 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}, journal={Journal of chemical theory and computation}, volume={11}, number={3}, pages={1063--1076}, year={2015}, publisher={American Chemical Society} } - 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, title={The impact of side-chain packing on protein docking refinement}, author={Moghadasi, Mohammad and Mirzaei, Hanieh and Mamonov, Artem and Vakili, Pirooz and Vajda, Sandor and Paschalidis, Ioannis Ch and Kozakov, Dima}, journal={Journal of chemical information and modeling}, volume={55}, number={4}, pages={872--881}, year={2015}, publisher={American Chemical Society} } - 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, title={New frontiers in druggability}, author={Kozakov, Dima and Hall, David R and Napoleon, Raeanne L and Yueh, Christine and Whitty, Adrian and Vajda, Sandor}, journal={Journal of medicinal chemistry}, volume={58}, number={23}, pages={9063--9088}, year={2015}, publisher={American Chemical Society} } - 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, title={Fragments and hot spots in drug discovery}, author={Vajda, Sandor and Whitty, Adrian and Kozakov, Dima}, journal={Oncotarget}, volume={6}, number={22}, pages={18740}, year={2015}, publisher={Impact Journals, LLC} } - 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, title={Lessons from hot spot analysis for fragment-based drug discovery}, author={Hall, David R and Kozakov, Dima and Whitty, Adrian and Vajda, Sandor}, journal={Trends in pharmacological sciences}, volume={36}, number={11}, pages={724--736}, year={2015}, publisher={Elsevier Current Trends} } - 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, title={Conservation and covariance in small bacterial phosphoglycosyltransferases identify the functional catalytic core}, author={Lukose, Vinita and Luo, Lingqi and Kozakov, Dima and Vajda, Sandor and Allen, Karen N and Imperiali, Barbara}, journal={Biochemistry}, volume={54}, number={50}, pages={7326--7334}, year={2015}, publisher={American Chemical Society} } - R. Mannhold, H. Kubinyi, and G. Folkers, Fragment-based drug discovery: lessons and outlookJohn Wiley & Sons, 2015.
[BibTeX]@misc{mannhold2015fragment, title={Fragment-based drug discovery: lessons and outlook}, author={Mannhold, Raimund and Kubinyi, Hugo and Folkers, Gerd}, year={2015}, publisher={John Wiley \& Sons} }
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, title={How proteins bind macrocycles}, 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}, volume={10}, number={9}, pages={723}, year={2014}, publisher={Nature Publishing Group} } - 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, title={Blind prediction of interfacial water positions in CAPRI}, 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}, volume={82}, number={4}, pages={620--632}, 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, title={Ligand Binding and Activation of PPAR $\gamma$ by Firemaster{\textregistered} 550: Effects on Adipogenesis and Osteogenesis in Vitro}, 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}, volume={122}, number={11}, pages={1225--1232}, year={2014}, publisher={NLM-Export} } - 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, title={Organization of the human mitochondrial transcription initiation complex}, 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}, volume={42}, number={6}, pages={4100--4112}, year={2014}, publisher={Oxford University Press} } - 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, title={Encounter complexes and dimensionality reduction in protein--protein association}, 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}, volume={3}, pages={e01370}, year={2014}, publisher={eLife Sciences Publications Limited} } - 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, title={Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces}, author={Bohnuud, Tanggis and Kozakov, Dima and Vajda, Sandor}, journal={PLoS computational biology}, volume={10}, number={10}, pages={e1003872}, year={2014}, publisher={Public Library of Science} } - 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, title={Insights into the architecture of the eIF2B$\alpha$/$\beta$/$\delta$ regulatory subcomplex}, 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}, volume={53}, number={21}, pages={3432--3445}, year={2014}, publisher={American Chemical Society} } - 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, title={Docking server for the identification of heparin binding sites on proteins}, 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}, volume={54}, number={7}, pages={2068--2078}, year={2014}, publisher={American Chemical Society} } - 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, title={Optimization on the space of rigid and flexible motions: an alternative manifold optimization approach}, 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}, pages={5825--5830}, year={2014}, organization={IEEE} } - 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, title={Efficient maintenance and update of nonbonded lists in macromolecular simulations}, 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}, volume={10}, number={10}, pages={4449--4454}, year={2014}, publisher={American Chemical Society} } - 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, title={A subspace semi-definite programming-based underestimation (ssdu) method for stochastic global optimization in protein docking}, 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}, pages={4623--4628}, year={2014}, organization={IEEE} } - 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, title={Stimulators of translation identified during a small molecule screening campaign}, 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}, volume={447}, pages={6--14}, year={2014}, publisher={Elsevier} } - 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, title={In silico identification of an aryl hydrocarbon receptor antagonist with biological activity in vitro and in vivo}, 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}, volume={86}, number={5}, pages={593--608}, year={2014}, publisher={American Society for Pharmacology and Experimental Therapeutics} }
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, title={How good is automated protein docking?}, 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}, volume={81}, number={12}, pages={2159--2166}, 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, title={Community-wide evaluation of methods for predicting the effect of mutations on protein--protein interactions}, 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}, volume={81}, number={11}, pages={1980--1987}, 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, title={Comprehensive experimental and computational analysis of binding energy hot spots at the NF-$\kappa$B Essential Modulator/IKK$\beta$ protein--protein Interface}, 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}, volume={135}, number={16}, pages={6242--6256}, year={2013}, publisher={American Chemical Society} } - 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, title={Sampling and scoring: A marriage made in heaven}, author={Vajda, Sandor and Hall, David R and Kozakov, Dima}, journal={Proteins: Structure, Function, and Bioinformatics}, volume={81}, number={11}, pages={1874--1884}, 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, title={Detection of peptide-binding sites on protein surfaces: The first step toward the modeling and targeting of peptide-mediated interactions}, 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}, volume={81}, number={12}, pages={2096--2105}, 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, title={FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots}, author={Grove, Laurie E and Hall, David R and Beglov, Dmitri and Vajda, Sandor and Kozakov, Dima}, journal={Bioinformatics}, volume={29}, number={9}, pages={1218--1219}, year={2013}, publisher={Oxford University Press} } - 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, title={A new distributed algorithm for side-chain positioning in the process of protein docking}, author={Moghadasi, Mohammad and Kozakov, Dima and Vakili, Pirooz and Vajda, Sandor and Paschalidis, Ioannis Ch}, booktitle={52nd IEEE Conference on Decision and Control}, pages={739--744}, year={2013}, organization={IEEE} } - 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, title={Flexible refinement of protein-ligand docking on manifolds}, 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}, pages={1392--1397}, year={2013}, organization={IEEE} } - 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, 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)}, 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}, year={2013}, publisher={Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology} }
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, title={Relationship between hot spot residues and ligand binding hot spots in protein--protein interfaces}, author={Zerbe, Brandon S and Hall, David R and Vajda, Sandor and Whitty, Adrian and Kozakov, Dima}, journal={Journal of chemical information and modeling}, volume={52}, number={8}, pages={2236--2244}, year={2012}, publisher={American Chemical Society} } - 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, title={FTMAP: extended protein mapping with user-selected probe molecules}, 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}, volume={40}, number={W1}, pages={W271--W275}, year={2012}, publisher={Oxford University Press} } - 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, title={Application of asymmetric statistical potentials to antibody--protein docking}, 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}, volume={28}, number={20}, pages={2608--2614}, year={2012}, publisher={Oxford University Press} } - 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, title={Minimal ensembles of side chain conformers for modeling protein--protein interactions}, 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}, volume={80}, number={2}, pages={591--601}, year={2012}, publisher={Wiley Subscription Services, Inc., A Wiley Company Hoboken} } - 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, title={Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde}, 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}, volume={40}, number={16}, pages={7644--7652}, year={2012}, publisher={Oxford University Press} } - 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, title={Rigid body energy minimization on manifolds for molecular docking}, 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}, volume={8}, number={11}, pages={4374--4380}, year={2012}, publisher={American Chemical Society} } - 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, title={A first-generation multi-functional cytokine for simultaneous optical tracking and tumor therapy}, 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}, volume={7}, number={7}, pages={e40234}, year={2012}, publisher={Public Library of Science} } - 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, title={Analysis of protein binding sites by computational solvent mapping}, author={Hall, David R and Kozakov, Dima and Vajda, Sandor}, booktitle={Computational drug discovery and design}, pages={13--27}, year={2012}, publisher={Springer, New York, NY} } - 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, title={A new approach to rigid body minimization with application to molecular docking}, 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)}, pages={2983--2988}, year={2012}, organization={IEEE} } - 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, title={A message passing approach to side chain positioning with applications in protein docking refinement}, 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)}, pages={2310--2315}, year={2012}, organization={IEEE} }
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, title={Structural conservation of druggable hot spots in protein--protein interfaces}, 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}, volume={108}, number={33}, pages={13528--13533}, year={2011}, publisher={National Academy of Sciences} } - 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, title={Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F}, 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}, volume={108}, number={3}, pages={1046--1051}, year={2011}, publisher={National Academy of Sciences} } - 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, title={Analysis of binding site hot spots on the surface of Ras GTPase}, 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}, volume={413}, number={4}, pages={773--789}, year={2011}, publisher={Elsevier} } - 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, title={FTSite: high accuracy detection of ligand binding sites on unbound protein structures}, author={Ngan, Chi-Ho and Hall, David R and Zerbe, Brandon and Grove, Laurie E and Kozakov, Dima and Vajda, Sandor}, journal={Bioinformatics}, volume={28}, number={2}, pages={286--287}, year={2011}, publisher={Oxford University Press} } - 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, title={Blocking eIF4E-eIF4G interaction as a strategy to impair coronavirus replication}, 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}, volume={85}, number={13}, pages={6381--6389}, year={2011}, publisher={American Society for Microbiology Journals} } - 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, title={Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery}, 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}, volume={52}, number={1}, pages={199--209}, year={2011}, publisher={American Chemical Society} } - 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, title={Evolutionary origins of the estrogen signaling system: insights from amphioxus}, 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}, volume={127}, number={3-5}, pages={176--188}, year={2011}, publisher={Pergamon} } - 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, title={Robust identification of binding hot spots using continuum electrostatics: application to hen egg-white lysozyme}, 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}, volume={133}, number={51}, pages={20668--20671}, year={2011}, publisher={American Chemical Society} }
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, title={Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13--19}, 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}, volume={78}, number={15}, pages={3124--3130}, year={2010}, publisher={Wiley Online Library} } - 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, title={Where does amantadine bind to the influenza virus M2 proton channel?}, author={Kozakov, Dima and Chuang, Gwo-Yu and Beglov, Dmitri and Vajda, Sandor}, journal={Trends in biochemical sciences}, volume={35}, number={9}, pages={471--475}, year={2010}, publisher={Elsevier Current Trends} } - 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, title={Domain motion and interdomain hot spots in a multidomain enzyme}, 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}, volume={19}, number={9}, pages={1662--1672}, year={2010}, publisher={Wiley Subscription Services, Inc., A Wiley Company Hoboken} }
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, title={Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques}, 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}, volume={25}, number={5}, pages={621--627}, year={2009}, publisher={Oxford University Press} } - 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, title={Convergence and combination of methods in protein--protein docking}, author={Vajda, Sandor and Kozakov, Dima}, journal={Current opinion in structural biology}, volume={19}, number={2}, pages={164--170}, year={2009}, publisher={Elsevier Current Trends} } - 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, title={Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase}, 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}, volume={23}, number={8}, pages={491--500}, year={2009}, publisher={Springer} } - 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, title={The structural basis of pregnane X receptor binding promiscuity}, author={Ngan, Chi-Ho and Beglov, Dmitri and Rudnitskaya, Aleksandra N and Kozakov, Dima and Waxman, David J and Vajda, Sandor}, journal={Biochemistry}, volume={48}, number={48}, pages={11572--11581}, year={2009}, publisher={American Chemical Society} } - 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, title={Binding hot spots and amantadine orientation in the influenza a virus M2 proton channel}, author={Chuang, Gwo-Yu and Kozakov, Dima and Brenke, Ryan and Beglov, Dmitri and Guarnieri, Frank and Vajda, Sandor}, journal={Biophysical journal}, volume={97}, number={10}, pages={2846--2853}, year={2009}, publisher={Elsevier} } - 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, title={Structural insights into recognition of $\beta$2-glycoprotein I by the lipoprotein receptors}, 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}, volume={77}, number={4}, pages={940--949}, year={2009}, publisher={Wiley Subscription Services, Inc., A Wiley Company Hoboken} } - 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, title={13 Identification of Druggable Hot Spots on Proteins and in Protein--Protein Interfaces}, 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}, year={2009}, publisher={CRC Press} } - J. Janin, “Basic principles of protein–protein interaction,” Computational protein–protein interactions, p. 1–20, 2009.
[BibTeX]@article{janin2009basic, title={Basic principles of protein--protein interaction}, author={Janin, Jo{\"e}l}, journal={Computational protein--protein interactions}, pages={1--20}, year={2009}, publisher={Taylor \& Francis Group New York, NY} }
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, title={Accelerating and focusing protein--protein docking correlations using multi-dimensional rotational FFT generating functions}, author={Ritchie, David W and Kozakov, Dima and Vajda, Sandor}, journal={Bioinformatics}, volume={24}, number={17}, pages={1865--1873}, year={2008}, publisher={Oxford University Press} } - 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, title={DARS (Decoys As the Reference State) potentials for protein-protein docking}, author={Chuang, Gwo-Yu and Kozakov, Dima and Brenke, Ryan and Comeau, Stephen R and Vajda, Sandor}, journal={Biophysical journal}, volume={95}, number={9}, pages={4217--4227}, year={2008}, publisher={Elsevier} } - 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, title={Discrimination of near-native structures in protein--protein docking by testing the stability of local minima}, author={Kozakov, Dima and Schueler-Furman, Ora and Vajda, Sandor}, journal={Proteins: Structure, Function, and Bioinformatics}, volume={72}, number={3}, pages={993--1004}, year={2008}, publisher={Wiley Online Library} }
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, title={ClusPro: performance in CAPRI rounds 6--11 and the new server}, 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}, volume={69}, number={4}, pages={781--785}, year={2007}, publisher={Wiley Subscription Services, Inc., A Wiley Company Hoboken} } - 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, title={Docking with PIPER and refinement with SDU in rounds 6--11 of CAPRI}, 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}, volume={69}, number={4}, pages={734--742}, year={2007}, publisher={Wiley-Blackwell} }
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, title={PIPER: an FFT-based protein docking program with pairwise potentials}, author={Kozakov, Dima and Brenke, Ryan and Comeau, Stephen R and Vajda, Sandor}, journal={Proteins: Structure, Function, and Bioinformatics}, volume={65}, number={2}, pages={392--406}, year={2006}, publisher={Wiley Online Library} } - 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, title={BIOT 194-New approaches to protein-protein docking}, 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}, volume={232}, year={2006}, organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA} }
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, title={Optimal clustering for detecting near-native conformations in protein docking}, author={Kozakov, Dima and Clodfelter, Karl H and Vajda, Sandor and Camacho, Carlos J}, journal={Biophysical journal}, volume={89}, number={2}, pages={867--875}, year={2005}, publisher={Cell Press} }