2024

• • Singh, A., Kundrotas, P.J., Vakser, I.A., 2024, Diffusion of proteins in crowded solutions studied by docking-based modeling, J. Chem. Phys., 161:095101.

• • Singh, A., Copeland, M.M., Kundrotas, P.J., Vakser, I.A., 2024, GRAMM webserver for protein docking, Methods Mol. Biol., 2714:101-112.

• • Collins, K.W., Copeland, M.M., Brysbaert, G., Wodak, S.J., Bonvin, A.M.J.J., Kundrotas, P.J., Vakser, I.A., Lensink, M.F., 2024, CAPRI-Q: The CAPRI resource for assessment of modeling protein interactions, J. Mol. Biol., 436:168540.

2023

• • Chen, S.J., et al. 2023, Protein folds vs protein folding: Differing questions, different challenges, Proc. Natl. Acad. Sci. USA, 120: e2214423119.

• • Vakser, I.A., 2023, Prediction of protein interactions is essential for studying biomolecular mechanisms, Proteomics, 23: e2300219.

2022

• • Kotthoff, I., Kundrotas, P.J., and Vakser, I.A., 2022, Dockground scoring benchmarks for protein docking, Proteins, 90:1259-1266.

• • Kotthoff, I., Kundrotas, P.J., Vakser, I.A., 2022, DOCKGROUND membrane protein-protein set, PLoS ONE, 17: e0267531.

• • Malladi, S., Powell, H.R., David, A., Islam, S.A., Copeland, M.M., Kundrotas, P.J., Sternberg, M.J.E., and Vakser, I.A., 2022, GWYRE: A resource for mapping variants onto experimental and modeled structures of human protein complexes, J. Mol.Biol., 434: 167608.

• • Vakser, I.A., Grudinin, S., Jenkins, N.W., Kundrotas, P.J., and Deeds, E.J. 2022, Docking-based long timescale simulation of cell-size protein systems at atomic resolution, Proc. Natl. Acad. Sci. USA, 119: e2210249119.

• • Collins, K.W., Copeland, M.M., Kotthoff, I., Singh, A., Kundrotas, P.J., and Vakser, I.A., 2022, DOCKGROUND resource for protein recognition studies, Prot. Sci., 31: e4481.

• • Jenkins, N.W., Kundrotas, P.J., and Vakser, I.A., 2022, Size of the protein-protein energy funnel in crowded environment, Front. Mol. Biosci., 9: 1031225.

2021

• • Badal, V.D., Kundrotas, P.J., Vakser, I.A., 2021, Text mining for modeling of protein complexes enhanced by machine learning, Bioinformatics, 37:497-505.

• • Hadarovich, A., Chakravarty, D., Tuzikov, A.V., Ben-Tal, N., Kundrotas, P.J., Vakser, I.A., 2021, Structural motifs in protein cores and at protein-protein interfaces are different, Prot. Sci., 30:381-390.

• • Lensink, M.F. et al. 2021, Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment, Proteins, 89: 1800-1823.

2020

• • Kundrotas, P.J., Kotthoff, I., Choi, S.W., Copeland, M.M., Vakser, I.A., 2020, DOCKGROUND tool for development and benchmarking of protein docking procedures, Methods in Mol. Biol., 2165:289-300.

• • Chakravarty, D., McElfresh, G.W., Kundrotas, P.J., Vakser, I.A., 2020, How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking, Proteins, 88:1070-1081.

• • Singh, A., Dauzhenka, T., Kundrotas, P.J., Sternberg, M.J.E., Vakser, I.A., 2020, Application of docking methodologies to modeled proteins, Proteins, 88:1180-1188.

• • Vakser, I.A., 2020, Challenges in protein docking, Curr. Opin. Struc. Biol., 64: 160-165.

2019

• • Hadarovich, A., Anishchenko, I., Tuzikov, A.V., Kundrotas, P.J., Vakser, I.A., 2019, Gene ontology improves template selection in comparative protein docking, Proteins, 87: 245-253

• • Vakser, I.A., Deeds, E.J., 2019, Computational approaches to macromolecular interactions in the cell, Curr. Opin. Struct. Biol., 55: 59-65.

• • Ofoegbu, T.C., David, A., Kelley, L., Mezulis, S., Islam, S., Mersmann, S., Stroemich, L., Vakser, I.A., Houlston, R., Sternberg, M.J.E., 2019, PhyreRisk: A dynamic web application to bridge genomics, proteomics and 3D structural data to guide interpretation of human genetic variants, J. Mol. Biol., 431:2460-2466.

• • Vakser I.A, Joachimiak A., 2019 Editorial overview: Macromolecular assemblies, Curr. Opin. Struct. Biol., 55:iii-v.

• • Lensink, M.F. et al., 2019, , Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment, Proteins, 87:1200-1221.

2018

• • Kundrotas, P.J., Anishchenko, I., Dauzhenka, T., Kotthoff, I., Mnevets, D., Copeland, M.M., Vakser, I.A., 2018, DOCKGROUND: a comprehensive data resource for modeling of protein complexes, Protein Sci., 27:172-181.

• • Kundrotas, P.J., Anishchenko, I., Badal, V., Das, M., Dauzhenka, T., and Vakser, I.A., 2018, Modeling CAPRI targets 110 - 120 by template-based and free docking using contact potential and combined scoring function, Proteins, 86: 302-310.

• • Badal, V.D., Kundrotas, P.J., Vakser, I.A., 2018, Natural language processing in text mining for structural modeling of protein complexes, BMC Bioinformatics, 19: 84.

• • Belkin, S., Kundrotas, P.J., Vakser, I.A., 2018, Inhibition of protein interactions: Co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking, J. Comput. Aided Mol. Des., 32: 769-779.

• • Dauzhenka, T., Kundrotas, P.J., Vakser, I.A., 2018, Computational feasibility of an exhaustive search of side-chain conformations in protein-protein docking, J. Comput. Chem., 39: 2012-2021.

• • Anishchenko, I., Kundrotas, P.J., Vakser, I.A., 2018, Contact potential for structure prediction of proteins and protein complexes from Potts model, Biophys. J., 115: 809-821.

2017

• • Anishchenko, I., Kundrotas, P.J., Vakser, I.A., 2017, Modeling Complexes of Modeled Proteins, Proteins, 85: 470-478.

• • Anishchenko, I., Kundrotas, P.J., Vakser, I.A., 2017, Structural quality of unrefined models in protein docking, Proteins, 85: 39-45.

• • Nussinov, R., Papin, J.A., Vakser, I.A., 2017, Computing the dynamic supramolecular structural proteome, PLoS Comp. Biol., 13: e1005290.

2016

• • Lensink, M.F. et al., 2016, Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment, Proteins, 84(Suppl 1):323-348.

• • Im, W., Liang, J., Olson, A., Zhou, H.X., Vajda, S., Vakser, I.A., 2016, Challenges in structural approaches to cell modeling, J. Mol. Biol. 428:2943-2964.

• • Anishchenko, I., Badal, V.D., Dauzhenka, T., Das, M., Tuzikov, A.V., Kundrotas, P.J., Vakser, I.A., 2016, Genome-wide structural modeling of protein-protein interactions, in: Bioinformatics Research and Applications (Bourgeois, Skums, Wan & Zelikovsky, eds.) Springer, pp. 95-105.

• • Zheng, J., Kundrotas, P.J., Vakser, I.A., Liu, S., 2016, Template-based modeling of protein-RNA interactions, PLoS Comp.Biol. 12:e1005120.

2015

• • Anishchenko, I., Kundrotas, P.J., Tuzikov, A.V., Vakser, I.A., 2015, Protein models docking benchmark 2, Proteins, 83: 891-897.

• • Anishchenko, I., Kundrotas, P.J., Tuzikov, A.V., Vakser, I.A., 2015, Structural templates for comparative protein docking, Proteins, 83: 1563-1570.

• • Kirys, T., Ruvinsky, A.M., Singla, D., Tuzikov, A.V., Kundrotas, P.J., Vakser, I.A., 2015, Simulated unbound structures for benchmarking of protein docking in the DOCKGROUND resource, BMC Bioinformatics, 16:243.

• • Badal, V.D., Kundrotas, P.J., Vakser, I.A., 2015, Text mining for protein docking, PLoS Comp.Biol. 11: e1004630.

• • Hadarovich, A., Anishchenko, I., Kundrotas, P.J., Tuzikov, A.V., Vakser, I.A., 2015, Quantitative comparison of functional properties in protein-protein complexes, in: Proc. MCCMB, Moscow

2014

• • Anishchenko, I., Kundrotas, P.J., Tuzikov, A.V., Vakser, I.A., 2014, Protein models: The Grand Challenge of protein docking, Proteins, 82: 278-287.

• • Lensink, M.F. et al., 2014, Blind prediction of interfacial water positions in CAPRI. Proteins, 82: 620-632.

• • Ruvinsky, A.M., Vakser, I.A., Rivera, M., 2014, Local packing modulates diversity of iron pathways and cooperative behavior in eukaryotic and prokaryotic ferritins, J. Chem. Phys., 140: 115104.

• • Vakser, I.A., 2014, Protein-protein docking: From interaction to interactome, Biophys. J., 107: 1785-1793.

2013

• • Vakser, I.A., 2013, Low-resolution structural modeling of protein interactome, Curr. Opin. Struc. Biol., 23: 198-205.

• • Ruvinsky, A.M., Kirys, T., Tuzikov, A.V., Vakser, I.A., 2013, Ensemble-based characterization of unbound and bound states on protein energy landscape, Protein Sci., 22: 734-744.

• • Kundrotas, P.J., Vakser, I.A., 2013, Protein-protein alternative binding modes do not overlap, Protein Sci., 22: 1141-1145 (Highlighted in "This Issue" section).

• • Kundrotas, P.J., Vakser, I.A., Janin, J., 2013, Structural templates for modeling homodimers, Protein Sci., 22: 1655-1663.

• • Kundrotas, P.J., Vakser, I.A., 2013, Global and local structural similarity in protein-protein complexes: Implications for template-based docking, Proteins, 81: 2137-2142.

2012

• • Sinha, R., Kundrotas, P.J., Vakser, I.A., 2012, Protein docking by the Interface Structure Similarity: How much structure is needed?, PLoS ONE. 7: e0031349.

• • Ruvinsky, A.M., Kirys, T., Tuzikov, A.V., Vakser, I.A., 2012, Structure fluctuations and conformational changes in protein binding, J. Bioinformatics Comput. Biol., 10: 1241002.

• • Kirys, T., Ruvinsky, A.M., Tuzikov, A.V., Vakser, I.A., 2012, Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding, Proteins, 80: 2089-2098.

• • Kundrotas, P.J., Zhu, Z., Janin, J., Vakser, I.A., 2012, Templates are available to model nearly all complexes of structurally characterized proteins, Proc. Natl. Acad. Sci. USA, 109; 9438-9441.

• • Yao, H., Wang, Y., Lovell, S., Kumar, R., Ruvinsky, A.M., Battaile, K.P., Vakser, I.A., Rivera, M., 2012, The structure of the BfrB-Bfd complex reveals protein-protein interactions enabling iron release from bacterioferritin, J. Amer. Chem. Soc., 134: 13470-13481 (Highlighted in Nature Chemical Biology, October, 2012).

• • Kirys, T., Ruvinsky, A.M., Tuzikov, A.V., Vakser, I.A., 2012, Correlation analysis of the side-chains conformation distributions in bound and unbound proteins, BMC Bioinformatics, 13: 236.

• • Kundrotas, P.J., Zhu, Z., Vakser, I.A., 2012, GWIDD: A comprehensive resource for genome-wide structural modeling of protein-protein interactions, Human Genomics, 6: 7.

2011

• • Ruvinsky, A.M., Kirys, T., Tuzikov, A.V., Vakser, I.A., 2011, Side-chain conformational changes upon protein-protein association, J.Mol.Biol., 408: 356-365.

• • Liu, S., Vakser, I.A., 2011, DECK: Distance and environment-dependent coarse-grained knowledge-based potentials for protein-protein docking, BMC Bioinformatics, 12:280.

• • Ruvinsky, A.M., Vakser, I.A., 2011, Structure fluctuations and configuration instabilities in proteins, in: Proc. MCCMB, Moscow, pp. 330-331.

2010

• • Kundrotas, P.J., Zhu, Z., Vakser, I.A., 2010, GWIDD: Genome-Wide Protein Docking Database, Nucl. Acids Res., 38:D513-517.

• • Kundrotas, P.J., Vakser, I.A., 2010, Accuracy of protein-protein binding sites in high-throughput template-based modeling, PLoS Comp. Biol. 6: e1000727.

• • Sinha, R., Kundrotas, P.J., Vakser, I.A., 2010, Docking by structural similarity at protein-protein interfaces, Proteins, 78: 3235-3241.

• • Ruvinsky, A.M., Vakser, I.A., 2010, Sequence composition and environment effects on residue fluctuations in protein structures, J. Chem. Phys., 133:155101 (Cover story; JCP Top 6 Most Downloaded Articles in October 2010).

2009

• • Ruvinsky, A.M., Vakser, I.A., 2009, The ruggedness of protein-protein energy landscape and the cutoff for 1/rn potentials, Bioinformatics, 25:1132-1136.

• • Vakser, I.A., 2009, Low-resolution recognition factors determine major characteristics of the energy landscape in protein-protein interaction, in: Computational Protein-Protein Interactions, Taylor and Francis, CRC press, pp.21-42.

• • Kirys, T., Ruvinsky, A., Tuzikov, A., Vakser, I.A., 2009, Conformational analysis of rotamer changes upon protein-protein binding, in: Proc. MCCMB, Moscow.

2008

• • O’Toole, N., Vakser, I.A., 2008, Large-scale characteristics of the energy landscape in protein-protein interactions, Proteins, 71:144-152.

• • Ruvinsky, A.M., Vakser, I.A., 2008, Interaction cutoff effect on ruggedness of protein-protein energy landscape, Proteins, 70:1498-1505.

• • Hunjan, J., Tovchigrechko, A., Gao, Y., Vakser, I.A., 2008, The size of the intermolecular energy funnel in protein-protein interactions, Proteins, 72:344–352.

• • Zhu, Z., Tovchigrechko, A., Baronova, T., Gao, Y., Douguet, D., O’Toole, N., Vakser, I.A., 2008, Large-scale structural modeling of protein complexes at low resolution, J. Bioinformatics Comp. Biol., 6:789–810.

• • Vakser, I.A., 2008, PSI has to live and become PCI - Protein Complex Initiative, Structure, 16:1-3.

• • Vakser, I.A., Kundrotas, P., 2008, Predicting 3D structures of protein-protein complexes, Curr. Pharm. Biotech., 9:57-66.

• • Ruvinsky, A.M., Vakser, I.A., 2008, Chasing funnels on protein-protein energy landscapes at different resolutions, Biophys. J., 95:2150–2159.

• • Liu, S., Gao, Y., Vakser, I.A., 2008, Dockground protein-protein docking decoy set, Bioinformatics, 2008; 24(22):2634-2635.

2007

• • Nicola, G., Vakser, I.A., 2007, A simple shape characteristic of protein-protein recognition, Bioinformatics, 23:789-792.

• • Vakser, I.A., Tovchigrechko, A., Zhu, Z., Hunjan, J., Ruvinsky, A., Gao, Y., 2007, Modeling of protein-protein interactions in structural genomics, in: Proc. MCCMB, Moscow, pp. 305-307.

• • Gao, Y., Douguet, D., Tovchigrechko, A., Vakser, I.A., 2007, Dockground system of databases for protein recognition studies: Unbound structures for docking, Proteins, 69:845-851.

2006

• • Tovchigrechko, A., Vakser, I.A., 2006, GRAMM-X public web server for protein-protein docking, Nucleic Acids Res, 34:W310-4.

• • Douguet, D., Chen, H.-C., Tovchigrechko, A., and Vakser, I.A., 2006, Dockground resource for studying protein-protein interfaces, Bioinformatics, 22:2612-2618.

2005

• • Marshall, G.R., Vakser, I.A., 2005, Protein-protein docking methods, in: Proteomics and Protein-Protein Interactions: Biology, Chemistry, Bioinformatics, And Drug Design (G.Waksman, ed.), in press.

• • Tovchigrechko, A., Vakser, I.A., 2005, Development and testing of an automated approach to protein docking, Proteins, 60:296-301.

2004

• • Jiang, S., Vakser, I.A., 2004, Shorter side chains optimize helix-helix packing, Protein Sci., 13:1426-1429.

• • Vakser, I.A., 2004, Protein-protein interfaces are special, Structure, 12:910-912.

2003

• • Janin, J., Henrick, K., Moult, J., Ten Eyck, L.F., Sternberg, M.J.E., Vajda, S., Vakser, I.A., Wodak, S.J. 2003, CAPRI: A Critical Assessment of PRedicted Interactions, Proteins, 52:2-9.

• • Jiang, S., Tovchigrechko, A., Vakser, I.A., 2003, The role of geometric complementarity in secondary structure packing: A systematic docking study, Protein Sci., 12: 1646-1651.

2002

• • Vakser, I.A., Jiang, S., 2002, Strategies for modeling the interactions of transmembrane helices of G protein-coupled receptors by geometric complementarity using the GRAMM computer algorithm, Methods Enzym., 343:313-328.

• • Vajda, S., Vakser, I.A., Sternberg, M.J.E., Janin, J., 2002, Modeling of protein interactions in genomes, Proteins, 47: 444-446.

• • Tovchigrechko, A., Wells, C.A., Vakser, I.A., 2002, Docking of protein models, Protein Sci., 11:1888-1896.

2001

• • Glaser, F., Steinberg, D., Vakser, I.A., Ben-Tal, N., 2001, Residue frequencies and pairing preferences at protein-protein interfaces, Proteins, 43:89-102.

• • Tovchigrechko, A., Vakser, I.A., 2001, How common is the funnel-like energy landscape in protein-protein interactions? Protein Sci., 10:1572-1583.

2000

• • Jiang, S., Vakser, I.A., 2000, Side chains in transmembrane helices are shorter at helix-helix interfaces, Proteins, 40:429-435.

1999

• • Vakser, I.A., Matar, O.G., Lam, C.F., 1999, A systematic study of low-resolution recognition in protein-protein complexes, Proc. Natl. Acad. Sci. USA , 96:8477-8482.

1998

• • Bridges, A., Gruenke, L., Chang, Y.-T., Vakser, I.A., Loew, G., Waskell, L., 1998, Identification of the binding site on cytochrome P450 2B4 for cytochrome b5 and cytochrome P450 reductase, J. Biol. Chem., 273:17036-17049.

1997

• • Chang, Y.-T., Stiffelman, O.B., Vakser, I.A., Loew, G.H., Bridges, A., Waskell, L., 1997, Construction of a 3D model of cytochrome P450 2B4, Protein Eng. , 10:119-129.

• • Vakser, I.A., 1997, Evaluation of GRAMM low-resolution docking methodology on hemagglutinin-antibody complex, Proteins, Suppl.1:226-230.

1996

• • Galaktionov, S.G., Tseytin, V.M., Vakser, I.A., Marshall, G.R., 1996, Calculation of peptide orientation at a lipophilic surface: An useful tool for "conformation-function" analysis, in: Peptides: Chemistry, Structure and Biology (Kaumaya, ed.), ESCOM, Leiden, pp. 507-508.

• • Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C., Vakser, I.A., 1996, The role of geometric fit between protein molecules and their ligands in determining biological specificity, Adv. Molec. Cell Biol., 15B:623-637.

• • Vakser, I.A., 1996, Low-resolution docking: Prediction of complexes for underdetermined structures, Biopolymers, 39:455-464.

• • Vakser, I.A., 1996, Long-distance potentials: An approach to the multiple-minima problem in ligand-receptor interaction, Protein Eng., 9:37-41.

• • Vakser, I.A., 1996, Main-chain complementarity in protein-protein recognition, Protein Eng., 9:741-744.

1995

• • Vakser, I.A., Nikiforovich, G.V., 1995, Protein docking in the absence of detailed molecular structures, in: Methods in Protein Structure Analysis (Atassi & Appella, eds.), Plenum Press, New York, pp. 505-514.

• • Vakser, I.A., 1995, Protein docking for low-resolution structures, Protein Eng., 8:371- 377.

1994

• • Vakser, I.A., Aflalo, C., 1994, Hydrophobic docking: A proposed enhancement to molecular recognition techniques, Proteins, 20:320-329.

1992

• • Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C., Vakser, I.A., 1992, Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques, Proc. Natl. Acad. Sci. USA, 89:2195-2199.

• • Tseytin, V.M., Vakser, I.A., Galaktionov, S.G., 1992, Interaction of peptide and protein molecules with lipophilic environment, in: Modelling and Computer Methods in Molecular Biology and Genetics (Ratner, ed.) Nova Science, New York, pp. 225-230.

1989

• • Galaktionov, S.G., Tseytin, V.M., Vakser, I.A., 1989, Calculation of stable conformations of peptide molecules in a heterogeneous environment, in: Chemistry and Biotechnology of Biologically Active Natural Products, Varna, pp. 302-307.

1988

• • Galaktionov, S.G., Tseytin, V.M., Vakser, I.A. et al., 1988, Amphiphilic properties of angiotensin and its fragments, Biophysics, 33:595-598.