Performance and Its Limits in Rigid Body Protein-Protein Docking von Desta, Israel T., Porter, Kathryn A., Xia, Bing, Kozakov, Dima, Vajda, Sandor

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The ClusPro web server for protein–protein docking von Kozakov, Dima, Hall, David R, Xia, Bing, Porter, Kathryn A, Padhorny, Dzmitry, Yueh, Christine, Beglov, Dmitri, Vajda, Sandor

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Convergence and combination of methods in protein–protein docking von Vajda, Sandor, Kozakov, Dima

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How good is automated protein docking? von Kozakov, Dima, Beglov, Dmitri, Bohnuud, Tanggis, Mottarella, Scott E., Xia, Bing, Hall, David R., Vajda, Sandor

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New additions to the ClusPro server motivated by CAPRI von Vajda, Sandor, Yueh, Christine, Beglov, Dmitri, Bohnuud, Tanggis, Mottarella, Scott E., Xia, Bing, Hall, David R., Kozakov, Dima

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The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins von Kozakov, Dima, Grove, Laurie E, Hall, David R, Bohnuud, Tanggis, Mottarella, Scott E, Luo, Lingqi, Xia, Bing, Beglov, Dmitri, Vajda, Sandor

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High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock von Alam, Nawsad, Goldstein, Oriel, Xia, Bing, Porter, Kathryn A, Kozakov, Dima, Schueler-Furman, Ora

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Accounting for pairwise distance restraints in FFT-based protein-protein docking von Xia, Bing, Vajda, Sandor, Kozakov, Dima

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Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery von Havugimana, Pierre C., Goel, Raghuveera Kumar, Phanse, Sadhna, Youssef, Ahmed, Padhorny, Dzmitry, Kotelnikov, Sergei, Kozakov, Dima, Emili, Andrew

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Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations von Wang, Jinan, Alekseenko, Andrey, Kozakov, Dima, Miao, Yinglong

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Exploring the structural origins of cryptic sites on proteins von Beglov, Dmitri, Hall, David R., Wakefield, Amanda E., Luo, Lingqi, Allen, Karen N., Kozakov, Dima, Whitty, Adrian, Vajda, Sandor

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Accelerating and focusing protein–protein docking correlations using multi-dimensional rotational FFT generating functions von Ritchie, David W., Kozakov, Dima, Vajda, Sandor

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Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques von Brenke, Ryan, Kozakov, Dima, Chuang, Gwo-Yu, Beglov, Dmitri, Hall, David, Landon, Melissa R., Mattos, Carla, Vajda, Sandor

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Structural conservation of druggable hot spots in protein–protein interfaces von Kozakov, Dima, Hall, David R, Chuang, Gwo-Yu, Cencic, Regina, Brenke, Ryan, Grove, Laurie E, Beglov, Dmitri, Pelletier, Jerry, Whitty, Adrian, Vajda, Sandor

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Application of asymmetric statistical potentials to antibody―protein docking von BRENKE, Ryan, HALL, David R, CHUANG, Gwo-Yu, COMEAU, Stephen R, BOHNUUD, Tanggis, BEGLOV, Dmitri, SCHUELER-FURMAN, Ora, VAJDA, Sandor, KOZAKOV, Dima

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Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19 von Kozakov, Dima, Hall, David R., Beglov, Dmitri, Brenke, Ryan, Comeau, Stephen R., Shen, Yang, Li, Keyong, Zheng, Jiefu, Vakili, Pirooz, Paschalidis, Ioannis Ch, Vajda, Sandor

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Ligand deconstruction: Why some fragment binding positions are conserved and others are not von Kozakov, Dima, Hall, David R., Jehle, Stefan, Luo, Lingqi, Ochiana, Stefan O., Jones, Elizabeth V., Pollastri, Michael, Allen, Karen N., Whitty, Adrian, Vajda, Sandor

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Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds von Padhorny, Dzmitry, Kazennov, Andrey, Zerbe, Brandon S., Porter, Kathryn A., Xia, Bing, Mottarella, Scott E., Kholodov, Yaroslav, Ritchie, David W., Vajda, Sandor, Kozakov, Dima

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Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein–Protein Interfaces von Zerbe, Brandon S, Hall, David R, Vajda, Sandor, Whitty, Adrian, Kozakov, Dima

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Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces von Bohnuud, Tanggis, Kozakov, Dima, Vajda, Sandor

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