Publications

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 cluspro 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 ClusPro 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. 255–278, 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--278},
    year={2017},
    publisher={Nature Research}
    }

  • 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, p. btx216, 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},
    pages={btx216},
    year={2017},
    publisher={Oxford University Press}
    }

2016

  • A. B. Mamonov, M. Moghadasi, H. Mirzaei, S. Zarbafian, L. E. Grove, T. Bohnuud, P. Vakili, S. Vajda, D. Kozakov, and others, “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 Vajda, Sandor and Kozakov, Dima and others},
    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, iss. S1, 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},
    number={S1},
    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 Acad Sciences}
    }

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,
    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--755},
    year={2015},
    publisher={Nature Research}
    }

  • 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 Acad 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}
    }

  • 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}
    }

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. 723–731, 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--731},
    year={2014},
    publisher={Nature Research}
    }

  • M. F. Lensink, I. H. Moal, P. A. Bates, P. L. Kastritis, A. S. Melquiond, E. Karaca, C. Schmitz, M. 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 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, 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},
    year={2014},
    publisher={National Institute of Environmental Health Science}
    }

  • 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}
    }

  • 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}
    }

  • S. Vajda, D. Kozakov, D. Beglov, I. C. Paschalidis, and P. Vakili, “Analysis of energy landscapes governing protein-protein association,” in Abstracts of papers of the american chemical society, 2014.
    [BibTeX]
    @inproceedings{vajda2014analysis,
    title={Analysis of energy landscapes governing protein-protein association},
    author={Vajda, Sandor and Kozakov, Dima and Beglov, Dmitri and Paschalidis, Ioannis Ch and Vakili, Pirooz},
    booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
    volume={247},
    year={2014},
    organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
    }

  • 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={ASPET}
    }

  • T. Bohnuud, D. Kozakov, and S. Vajda, “Evidence of conformational selection driving the formation of ligand binding sites in protein-protein,” , 2014.
    [BibTeX]
    @article{bohnuud2014evidence,
    title={Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein},
    author={Bohnuud, T and Kozakov, D and Vajda, S},
    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,
    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},
    publisher={Wiley Online Library}
    }

  • 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},
    publisher={Wiley Online Library}
    }

  • 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}
    }

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, 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, 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 Online Library}
    }

  • 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}
    }

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 Acad 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 Acad 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={Am Soc Microbiol}
    }

  • 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, 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},
    pages={176--188},
    year={2011},
    publisher={Elsevier}
    }

  • 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}
    }

  • 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 (vol 108, pg 1046, 2010),” Proceedings of the national academy of sciences of the united states of america, vol. 108, iss. 16, p. 6689–6689, 2011.
    [BibTeX]
    @article{cencic2011reversing,
    title={Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F (vol 108, pg 1046, 2010)},
    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 OF THE UNITED STATES OF AMERICA},
    volume={108},
    number={16},
    pages={6689--6689},
    year={2011},
    publisher={NATL ACAD SCIENCES 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA}
    }

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}
    }

  • 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 Online Library}
    }

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 Online Library}
    }

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 Online Library}
    }

  • 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 Online Library}
    }

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}
    }

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={Elsevier}
    }