I. Vakser

Most-cited papers

Protein-protein docking: from interaction to interactome.
I. Vakser
2014Biophysical Journal296 citations Open access
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Templates are available to model nearly all complexes of structurally characterized proteins
P. Kundrotas, Zhengwei Zhu, J. Janin, I. Vakser
2012Proceedings of the National Academy of Sciences of the United States of America188 citations Open access
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Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment
M. Lensink, S. Velankar, A. Kryshtafovych, Shengua Huang +98 more
2016Proteins: Structure, Function, and Bioinformatics133 citations Open access
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Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment
M. Lensink, G. Brysbaert, Théo Mauri, Nurul Nadzirin +104 more
2021Proteins: Structure, Function, and Bioinformatics104 citations Open access
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Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment
M. Lensink, G. Brysbaert, Nurul Nadzirin, S. Velankar +101 more
2019Proteins: Structure, Function, and Bioinformatics104 citations Open access
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Docking by structural similarity at protein-protein interfaces
Rohita Sinha, P. Kundrotas, I. Vakser
2010Proteins: Structure, Function, and Bioinformatics91 citations Open access
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The structure of the BfrB-Bfd complex reveals protein-protein interactions enabling iron release from bacterioferritin
H. Yao, Yan Wang, S. Lovell, Ritesh Kumar +4 more
2012Journal of the American Chemical Society88 citations Open access
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Protein folds vs. protein folding: Differing questions, different challenges
Shi-Jie Chen, Mubashir Hassan, R. Jernigan, Ke-Jue Jia +20 more
2022Proceedings of the National Academy of Sciences of the United States of America85 citations Open access
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Dockground: A comprehensive data resource for modeling of protein complexes
P. Kundrotas, I. Anishchenko, T. Dauzhenka, Ian Kotthoff +3 more
2018Protein Science83 citations Open access
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DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking
Ying Gao, D. Douguet, A. Tovchigrechko, I. Vakser
2007Proteins: Structure, Function, and Bioinformatics80 citations
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DOCKGROUND protein-protein docking decoy set
Shiyong Liu, Ying Gao, I. Vakser
2008Bioinform.72 citations Open access
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Blind Prediction of Interfacial Water Positions in CAPRI
M. Lensink, I. Moal, Paul A. Bates, P. Kastritis +54 more
2013Proteins: Structure, Function, and Bioinformatics63 citations Open access
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Low-resolution structural modeling of protein interactome
I. Vakser
2013Current Opinion in Structural Biology60 citations Open access
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Challenges in structural approaches to cell modeling
W. Im, Jie Liang, A. Olson, Huan-Xiang Zhou +2 more
2016Journal of Molecular Biology56 citations Open access
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DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking
Shiyong Liu, I. Vakser
2011BMC Bioinformatics48 citations Open access
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Predicting 3D structures of protein-protein complexes.
I. Vakser, P. Kundrotas
2008Current Pharmaceutical Biotechnology48 citations
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GWIDD: Genome-wide protein docking database
P. Kundrotas, Zhengwei Zhu, I. Vakser
2009Nucleic Acids Res.47 citations Open access
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Challenges in Protein Docking
I. Vakser
2020Current Opinion in Structural Biology43 citations Open access
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Accuracy of Protein-Protein Binding Sites in High-Throughput Template-Based Modeling
P. Kundrotas, I. Vakser
2010PLoS Comput. Biol.43 citations Open access
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Global and local structural similarity in protein–protein complexes: Implications for template-based docking
P. Kundrotas, I. Vakser
2013Proteins: Structure, Function, and Bioinformatics40 citations Open access
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Template-Based Modeling of Protein-RNA Interactions
Jinfang Zheng, P. Kundrotas, I. Vakser, Shiyong Liu
2016PLoS Comput. Biol.38 citations Open access
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STRUCTURE FLUCTUATIONS AND CONFORMATIONAL CHANGES IN PROTEIN BINDING
A. M. Ruvinsky, Tatsiana Kirys, A. Tuzikov, I. Vakser
2011J. Bioinform. Comput. Biol.38 citations Open access
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CAPRI-Q: The CAPRI resource for assessment of modeling protein interactions
Keeley W. Collins, Matthew M. Copeland, G. Brysbaert, S. Wodak +4 more
2024Journal of Molecular Biology36 citations Open access
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Application of docking methodologies to modeled proteins
Amar Singh, T. Dauzhenka, P. Kundrotas, M. Sternberg +1 more
2020Proteins: Structure, Function, and Bioinformatics36 citations Open access
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Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?
Rohita Sinha, P. Kundrotas, I. Vakser
2012PLoS ONE36 citations Open access
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Side-Chain Conformational Changes upon Protein-Protein Association
A. M. Ruvinsky, Tatsiana Kirys, A. Tuzikov, I. Vakser
2010Journal of Molecular Biology35 citations Open access
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Structural templates for comparative protein docking
I. Anishchenko, P. Kundrotas, A. Tuzikov, I. Vakser
2015Proteins: Structure, Function, and Bioinformatics31 citations Open access
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Natural language processing in text mining for structural modeling of protein complexes
Varsha D. Badal, P. Kundrotas, I. Vakser
2018BMC Bioinformatics30 citations Open access
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Sequence composition and environment effects on residue fluctuations in protein structures.
A. M. Ruvinsky, I. Vakser
2009Journal of Chemical Physics28 citations Open access
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The size of the intermolecular energy funnel in protein–protein interactions
J. Hunjan, A. Tovchigrechko, Ying Gao, I. Vakser
2008Proteins: Structure, Function, and Bioinformatics28 citations
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Modeling Complexes of Modeled Proteins
I. Anishchenko, P. Kundrotas, I. Vakser
2016Proteins: Structure, Function, and Bioinformatics27 citations Open access
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Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding
Tatsiana Kirys, A. M. Ruvinsky, A. Tuzikov, I. Vakser
2012Proteins: Structure, Function, and Bioinformatics27 citations Open access
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PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants
T. C. Ofoegbu, A. David, L. Kelley, S. Mezulis +6 more
2019Journal of Molecular Biology26 citations Open access
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Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model.
I. Anishchenko, P. Kundrotas, I. Vakser
2018Biophysical Journal24 citations Open access
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Protein models: The Grand Challenge of protein docking
I. Anishchenko, P. Kundrotas, A. Tuzikov, I. Vakser
2013Proteins: Structure, Function, and Bioinformatics24 citations Open access
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Protein Models Docking Benchmark 2
I. Anishchenko, P. Kundrotas, A. Tuzikov, I. Vakser
2015Proteins: Structure, Function, and Bioinformatics23 citations Open access
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Text Mining for Protein Docking
Varsha D. Badal, P. Kundrotas, I. Vakser
2015PLoS Comput. Biol.22 citations Open access
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Large‐scale characteristics of the energy landscape in protein–protein interactions
N. O'Toole, I. Vakser
2008Proteins: Structure, Function, and Bioinformatics22 citations
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Dockground resource for protein recognition studies
Keeley W. Collins, Matthew M. Copeland, Ian Kotthoff, Amar Singh +2 more
2022Protein Science19 citations Open access
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Interaction cutoff effect on ruggedness of protein–protein energy landscape
A. M. Ruvinsky, I. Vakser
2007Proteins: Structure, Function, and Bioinformatics19 citations
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Docking-based long timescale simulation of cell-size protein systems at atomic resolution
I. Vakser, Sergei Grudinin, Nathan W. Jenkins, P. Kundrotas +1 more
2022bioRxiv18 citations Open access
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Structural templates for modeling homodimers
P. Kundrotas, I. Vakser, J. Janin
2013Protein Science18 citations Open access
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Modeling CAPRI Targets 110 – 120 by Template-Based and Free Docking Using Contact Potential and Combined Scoring Function
P. Kundrotas, I. Anishchenko, Varsha D. Badal, Madhurima Das +2 more
2017Proteins: Structure, Function, and Bioinformatics17 citations Open access
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Chasing funnels on protein-protein energy landscapes at different resolutions.
A. M. Ruvinsky, I. Vakser
2008Biophysical Journal16 citations Open access
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Simulated unbound structures for benchmarking of protein docking in the Dockground resource
Tatsiana Kirys, A. M. Ruvinsky, Deepak Singla, A. Tuzikov +2 more
2015BMC Bioinformatics15 citations Open access
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GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions
P. Kundrotas, Zhengwei Zhu, I. Vakser
2012Human Genomics15 citations Open access
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Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking
T. Dauzhenka, P. Kundrotas, I. Vakser
2018Journal of Computational Chemistry13 citations Open access
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Local packing modulates diversity of iron pathways and cooperative behavior in eukaryotic and prokaryotic ferritins.
A. M. Ruvinsky, I. Vakser, M. Rivera
2014Journal of Chemical Physics13 citations Open access
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Protein–protein alternative binding modes do not overlap
P. Kundrotas, I. Vakser
2013Protein Science13 citations Open access
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Diffusion of proteins in crowded solutions studied by docking-based modeling
Amar Singh, P. Kundrotas, I. Vakser
2024Journal of Chemical Physics11 citations Open access
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