Ilya A. Vakser is a biophysics researcher and expert in protein interactions and structural description of protein complexes. He is known for his contributions to the field of molecular modelling and bioinformatics. Vakser is currently a Full Professor and Director of the KU Center for Computational Biology at the University of Kansas.
Vakser received his PhD in biophysics from Moscow State University in 1989. He then underwent further training at the Weizmann Institute, Washington University, and the Rockefeller University.
Prior to joining the University of Kansas in 2005, Vakser served on the faculty of the Medical University of South Carolina as an Assistant Professor and Associate Professor. He also held a position as an Associate Professor at SUNY Stony Brook.
Vakser's research focuses on molecular modelling in the context of structural genomics and bioinformatics. His major goals are to develop approaches for modelling protein interactions and to reconstruct the network of connections between proteins in a genome. Vakser is particularly interested in understanding the fundamental principles of protein interaction and creating a structure-based description of genomes.
He is one of the authors of the FFT docking algorithm, a standard tool in the protein docking field, and he initiated the community-wide CAPRI protein docking competition.
Ilya Vakser Professor and Director, University of Kansas https://compbio.ku.edu/ Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. E Katchalski-Katzir, I Shariv, M Eisenstein, AA Friesem, C Aflalo, … Proceedings of the National Academy of Sciences 89 (6), 2195-2199, 1992 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:u5HHmVD_uO8C Cited by: 1373
GRAMM-X public web server for protein–protein docking A Tovchigrechko, IA Vakser Nucleic acids research 34 (suppl2), W310-W314, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationfor_view=4rSlPOIAAAAJ:IjCSPb-OGe4C Cited by: 847
CAPRI: a critical assessment of predicted interactions J Janin, K Henrick, J Moult, LT Eyck, MJE Sternberg, S Vajda, I Vakser, … Proteins: Structure, Function, and Bioinformatics 52 (1), 2-9, 2003 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:u-x6o8ySG0sC Cited by: 787
Residue frequencies and pairing preferences at protein–protein interfaces F Glaser, DM Steinberg, IA Vakser, N Ben‐Tal Proteins: Structure, Function, and Bioinformatics 43 (2), 89-102, 2001 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:d1gkVwhDpl0C Cited by: 478
Identification of the binding site on cytochrome P450 2B4 for cytochrome b 5 and cytochrome P450 reductase A Bridges, L Gruenke, YT Chang, IA Vakser, G Loew, L Waskell Journal of Biological Chemistry 273 (27), 17036-17049, 1998 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:2osOgNQ5qMEC Cited by: 336
Protein-protein docking: From interaction to interactome IA Vakser Biophysical journal 107 (8), 1785-1793, 2014 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:RYcK_YlVTxYC Cited by: 324
Protein docking for low-resolution structures IA Vakser Protein Engineering, Design and Selection 8 (4), 371-378, 1995 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:9yKSN-GCB0IC Cited by: 311
Hydrophobic docking: a proposed enhancement to molecular recognition techniques IA Vakser, C Aflalo Proteins: Structure, Function, and Bioinformatics 20 (4), 320-329, 1994 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:qjMakFHDy7sC Cited by: 245
Templates are available to model nearly all complexes of structurally characterized proteins PJ Kundrotas, Z Zhu, J Janin, IA Vakser Proceedings of the National Academy of Sciences 109 (24), 9438-9441, 2012 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:e5wmG9Sq2KIC Cited by: 220
A systematic study of low-resolution recognition in protein–protein complexes IA Vakser, OG Matar, CF Lam Proceedings of the National Academy of Sciences 96 (15), 8477-8482, 1999 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:UeHWp8X0CEIC Cited by: 219
Development and testing of an automated approach to protein docking A Tovchigrechko, IA Vakser Proteins: Structure, Function, and Bioinformatics 60 (2), 296-301, 2005 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:WF5omc3nYNoC Cited by: 198
Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: a CASP‐CAPRI experiment MF Lensink, S Velankar, A Kryshtafovych, SY Huang, … Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:SeFeTyx0c_EC Cited by: 168
Evaluation of GRAMM low‐resolution docking methodology on the hemagglutinin‐antibody complex IA Vakser Proteins: Structure, Function, and Bioinformatics 29 (S1), 226-230, 1997 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:Tyk-4Ss8FVUC Cited by: 158
Low‐resolution docking: prediction of complexes for underdetermined structures IA Vakser Biopolymers 39 (3), 455-464, 1996 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:zYLM7Y9cAGgC Cited by: 156
Docking of protein models A Tovchigrechko, CA Wells, IA Vakser Protein Science 11 (8), 1888-1896, 2002 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:Y0pCki6q_DkC Cited by: 127
Blind prediction of homo‐and hetero‐protein complexes: The CASP13‐CAPRI experiment MF Lensink, G Brysbaert, N Nadzirin, S Velankar, RAG Chaleil, T Gerguri, … Proteins: Structure, Function, and Bioinformatics 87 (12), 1200-1221, 2019 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:sSrBHYA8nusC Cited by: 118
How common is the funnel‐like energy landscape in protein‐protein interactions? A Tovchigrechko, IA Vakser Protein science 10 (8), 1572-1583, 2001 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:eQOLeE2rZwMC Cited by: 108
Dockground resource for studying protein–protein interfaces D Douguet, HC Chen, A Tovchigrechko, IA Vakser Bioinformatics 22 (21), 2612-2618, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:_FxGoFyzp5QC Cited by: 107
Docking by structural similarity at protein‐protein interfaces R Sinha, PJ Kundrotas, IA Vakser Proteins: Structure, Function, and Bioinformatics 78 (15), 3235-3241, 2010 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:Zph67rFs4hoC Cited by: 103
Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction IA Vakser Protein Engineering, Design and Selection 9 (1), 37-41, 1996 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:YsMSGLbcyi4C Cited by: 97
Petras Kundrotas JvYJSc4AAAAJ
Andrey Tovchigrechko ULtDvKYAAAAJ
Ivan Anishchenko Hp8zwAgAAAAJ
Alexander Tuzikov EL7ilZEAAAAJ
Anatoly M. Ruvinsky 09ZOiRYAAAAJ
Joel Janin R71twNgAAAAJ
M Sternberg TDuw5O0AAAAJ
Claude Aflalo AX2nYIwAAAAJ
Sandor Vajda _gYtig8AAAAJ
Zhengwei Zhu Y54z02YAAAAJ
Ilya Vakser Professor and Director, University of Kansas https://compbio.ku.edu/ Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. E Katchalski-Katzir, I Shariv, M Eisenstein, AA Friesem, C Aflalo, … Proceedings of the National Academy of Sciences 89 (6), 2195-2199, 1992 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:u5HHmVD_uO8C Cited by: 1373
GRAMM-X public web server for protein–protein docking A Tovchigrechko, IA Vakser Nucleic acids research 34 (suppl2), W310-W314, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationfor_view=4rSlPOIAAAAJ:IjCSPb-OGe4C Cited by: 847
CAPRI: a critical assessment of predicted interactions J Janin, K Henrick, J Moult, LT Eyck, MJE Sternberg, S Vajda, I Vakser, … Proteins: Structure, Function, and Bioinformatics 52 (1), 2-9, 2003 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:u-x6o8ySG0sC Cited by: 787
Residue frequencies and pairing preferences at protein–protein interfaces F Glaser, DM Steinberg, IA Vakser, N Ben‐Tal Proteins: Structure, Function, and Bioinformatics 43 (2), 89-102, 2001 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:d1gkVwhDpl0C Cited by: 478
Identification of the binding site on cytochrome P450 2B4 for cytochrome b 5 and cytochrome P450 reductase A Bridges, L Gruenke, YT Chang, IA Vakser, G Loew, L Waskell Journal of Biological Chemistry 273 (27), 17036-17049, 1998 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:2osOgNQ5qMEC Cited by: 336
Protein-protein docking: From interaction to interactome IA Vakser Biophysical journal 107 (8), 1785-1793, 2014 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:RYcK_YlVTxYC Cited by: 324
Protein docking for low-resolution structures IA Vakser Protein Engineering, Design and Selection 8 (4), 371-378, 1995 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:9yKSN-GCB0IC Cited by: 311
Hydrophobic docking: a proposed enhancement to molecular recognition techniques IA Vakser, C Aflalo Proteins: Structure, Function, and Bioinformatics 20 (4), 320-329, 1994 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:qjMakFHDy7sC Cited by: 245
Templates are available to model nearly all complexes of structurally characterized proteins PJ Kundrotas, Z Zhu, J Janin, IA Vakser Proceedings of the National Academy of Sciences 109 (24), 9438-9441, 2012 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:e5wmG9Sq2KIC Cited by: 220
A systematic study of low-resolution recognition in protein–protein complexes IA Vakser, OG Matar, CF Lam Proceedings of the National Academy of Sciences 96 (15), 8477-8482, 1999 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:UeHWp8X0CEIC Cited by: 219
Development and testing of an automated approach to protein docking A Tovchigrechko, IA Vakser Proteins: Structure, Function, and Bioinformatics 60 (2), 296-301, 2005 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:WF5omc3nYNoC Cited by: 198
Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: a CASP‐CAPRI experiment MF Lensink, S Velankar, A Kryshtafovych, SY Huang, … Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:SeFeTyx0c_EC Cited by: 168
Evaluation of GRAMM low‐resolution docking methodology on the hemagglutinin‐antibody complex IA Vakser Proteins: Structure, Function, and Bioinformatics 29 (S1), 226-230, 1997 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:Tyk-4Ss8FVUC Cited by: 158
Low‐resolution docking: prediction of complexes for underdetermined structures IA Vakser Biopolymers 39 (3), 455-464, 1996 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:zYLM7Y9cAGgC Cited by: 156
Docking of protein models A Tovchigrechko, CA Wells, IA Vakser Protein Science 11 (8), 1888-1896, 2002 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:Y0pCki6q_DkC Cited by: 127
Blind prediction of homo‐and hetero‐protein complexes: The CASP13‐CAPRI experiment MF Lensink, G Brysbaert, N Nadzirin, S Velankar, RAG Chaleil, T Gerguri, … Proteins: Structure, Function, and Bioinformatics 87 (12), 1200-1221, 2019 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:sSrBHYA8nusC Cited by: 118
How common is the funnel‐like energy landscape in protein‐protein interactions? A Tovchigrechko, IA Vakser Protein science 10 (8), 1572-1583, 2001 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:eQOLeE2rZwMC Cited by: 108
Dockground resource for studying protein–protein interfaces D Douguet, HC Chen, A Tovchigrechko, IA Vakser Bioinformatics 22 (21), 2612-2618, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:_FxGoFyzp5QC Cited by: 107
Docking by structural similarity at protein‐protein interfaces R Sinha, PJ Kundrotas, IA Vakser Proteins: Structure, Function, and Bioinformatics 78 (15), 3235-3241, 2010 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:Zph67rFs4hoC Cited by: 103
Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction IA Vakser Protein Engineering, Design and Selection 9 (1), 37-41, 1996 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:YsMSGLbcyi4C Cited by: 97
Petras Kundrotas googlescholarauthor_id:JvYJSc4AAAAJ
Andrey Tovchigrechko googlescholarauthor_id:ULtDvKYAAAAJ
Ivan Anishchenko googlescholarauthor_id:Hp8zwAgAAAAJ
Alexander Tuzikov googlescholarauthor_id:EL7ilZEAAAAJ
Anatoly M. Ruvinsky googlescholarauthor_id:09ZOiRYAAAAJ
Joel Janin googlescholarauthor_id:R71twNgAAAAJ
M Sternberg googlescholarauthor_id:TDuw5O0AAAAJ
Claude Aflalo googlescholarauthor_id:AX2nYIwAAAAJ
Sandor Vajda googlescholarauthorid:gYtig8AAAAJ
Zhengwei Zhu googlescholarauthor_id:Y54z02YAAAAJ
Ilya Vakser Professor and Director, University of Kansas https://compbio.ku.edu/ Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. E Katchalski-Katzir, I Shariv, M Eisenstein, AA Friesem, C Aflalo, … Proceedings of the National Academy of Sciences 89 (6), 2195-2199, 1992 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:u5HHmVD_uO8C Cited by: 1373
GRAMM-X public web server for protein–protein docking A Tovchigrechko, IA Vakser Nucleic acids research 34 (suppl2), W310-W314, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationfor_view=4rSlPOIAAAAJ:IjCSPb-OGe4C Cited by: 847
CAPRI: a critical assessment of predicted interactions J Janin, K Henrick, J Moult, LT Eyck, MJE Sternberg, S Vajda, I Vakser, … Proteins: Structure, Function, and Bioinformatics 52 (1), 2-9, 2003 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:u-x6o8ySG0sC Cited by: 787
Residue frequencies and pairing preferences at protein–protein interfaces F Glaser, DM Steinberg, IA Vakser, N Ben‐Tal Proteins: Structure, Function, and Bioinformatics 43 (2), 89-102, 2001 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:d1gkVwhDpl0C Cited by: 478
Identification of the binding site on cytochrome P450 2B4 for cytochrome b 5 and cytochrome P450 reductase A Bridges, L Gruenke, YT Chang, IA Vakser, G Loew, L Waskell Journal of Biological Chemistry 273 (27), 17036-17049, 1998 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:2osOgNQ5qMEC Cited by: 336
Protein-protein docking: From interaction to interactome IA Vakser Biophysical journal 107 (8), 1785-1793, 2014 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:RYcK_YlVTxYC Cited by: 324
Protein docking for low-resolution structures IA Vakser Protein Engineering, Design and Selection 8 (4), 371-378, 1995 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:9yKSN-GCB0IC Cited by: 311
Hydrophobic docking: a proposed enhancement to molecular recognition techniques IA Vakser, C Aflalo Proteins: Structure, Function, and Bioinformatics 20 (4), 320-329, 1994 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:qjMakFHDy7sC Cited by: 245
Templates are available to model nearly all complexes of structurally characterized proteins PJ Kundrotas, Z Zhu, J Janin, IA Vakser Proceedings of the National Academy of Sciences 109 (24), 9438-9441, 2012 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:e5wmG9Sq2KIC Cited by: 220
A systematic study of low-resolution recognition in protein–protein complexes IA Vakser, OG Matar, CF Lam Proceedings of the National Academy of Sciences 96 (15), 8477-8482, 1999 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:UeHWp8X0CEIC Cited by: 219
Development and testing of an automated approach to protein docking A Tovchigrechko, IA Vakser Proteins: Structure, Function, and Bioinformatics 60 (2), 296-301, 2005 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:WF5omc3nYNoC Cited by: 198
Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: a CASP‐CAPRI experiment MF Lensink, S Velankar, A Kryshtafovych, SY Huang, … Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:SeFeTyx0c_EC Cited by: 168
Evaluation of GRAMM low‐resolution docking methodology on the hemagglutinin‐antibody complex IA Vakser Proteins: Structure, Function, and Bioinformatics 29 (S1), 226-230, 1997 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:Tyk-4Ss8FVUC Cited by: 158
Low‐resolution docking: prediction of complexes for underdetermined structures IA Vakser Biopolymers 39 (3), 455-464, 1996 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:zYLM7Y9cAGgC Cited by: 156
Docking of protein models A Tovchigrechko, CA Wells, IA Vakser Protein Science 11 (8), 1888-1896, 2002 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:Y0pCki6q_DkC Cited by: 127
Blind prediction of homo‐and hetero‐protein complexes: The CASP13‐CAPRI experiment MF Lensink, G Brysbaert, N Nadzirin, S Velankar, RAG Chaleil, T Gerguri, … Proteins: Structure, Function, and Bioinformatics 87 (12), 1200-1221, 2019 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:sSrBHYA8nusC Cited by: 118
How common is the funnel‐like energy landscape in protein‐protein interactions? A Tovchigrechko, IA Vakser Protein science 10 (8), 1572-1583, 2001 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:eQOLeE2rZwMC Cited by: 108
Dockground resource for studying protein–protein interfaces D Douguet, HC Chen, A Tovchigrechko, IA Vakser Bioinformatics 22 (21), 2612-2618, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:_FxGoFyzp5QC Cited by: 107
Docking by structural similarity at protein‐protein interfaces R Sinha, PJ Kundrotas, IA Vakser Proteins: Structure, Function, and Bioinformatics 78 (15), 3235-3241, 2010 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:Zph67rFs4hoC Cited by: 103
Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction IA Vakser Protein Engineering, Design and Selection 9 (1), 37-41, 1996 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:YsMSGLbcyi4C Cited by: 97
Petras Kundrotas googlescholarauthorid petraskundrotas.md:JvYJSc4AAAAJ
Andrey Tovchigrechko googlescholarauthorid andreytovchigrechko.md:ULtDvKYAAAAJ
Ivan Anishchenko googlescholarauthorid ivananishchenko.md:Hp8zwAgAAAAJ
Alexander Tuzikov googlescholarauthorid alexandertuzikov.md:EL7ilZEAAAAJ
Anatoly M. Ruvinsky googlescholarauthorid anatolym._ruvinsky.md:09ZOiRYAAAAJ
Joel Janin googlescholarauthorid joeljanin.md:R71twNgAAAAJ
M Sternberg googlescholarauthorid msternberg.md:TDuw5O0AAAAJ
Claude Aflalo googlescholarauthorid claudeaflalo.md:AX2nYIwAAAAJ
Sandor Vajda googlescholarauthorid sandorvajda.md:_gYtig8AAAAJ
Zhengwei Zhu googlescholarauthorid zhengweizhu.md:Y54z02YAAAAJ
Ilya Vakser
Professor and Director, University of Kansas
https://compbio.ku.edu/
Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. E Katchalski-Katzir, I Shariv, M Eisenstein, AA Friesem, C Aflalo, … Proceedings of the National Academy of Sciences 89 (6), 2195-2199, 1992 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:u5HHmVD_uO8C
GRAMM-X public web server for protein–protein docking A Tovchigrechko, IA Vakser Nucleic acids research 34 (suppl2), W310-W314, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationfor_view=4rSlPOIAAAAJ:IjCSPb-OGe4C
CAPRI: a critical assessment of predicted interactions J Janin, K Henrick, J Moult, LT Eyck, MJE Sternberg, S Vajda, I Vakser, … Proteins: Structure, Function, and Bioinformatics 52 (1), 2-9, 2003 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:u-x6o8ySG0sC
Residue frequencies and pairing preferences at protein–protein interfaces F Glaser, DM Steinberg, IA Vakser, N Ben‐Tal Proteins: Structure, Function, and Bioinformatics 43 (2), 89-102, 2001 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:d1gkVwhDpl0C
Identification of the binding site on cytochrome P450 2B4 for cytochrome b 5 and cytochrome P450 reductase A Bridges, L Gruenke, YT Chang, IA Vakser, G Loew, L Waskell Journal of Biological Chemistry 273 (27), 17036-17049, 1998 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:2osOgNQ5qMEC
Protein-protein docking: From interaction to interactome IA Vakser Biophysical journal 107 (8), 1785-1793, 2014 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:RYcK_YlVTxYC
Protein docking for low-resolution structures IA Vakser Protein Engineering, Design and Selection 8 (4), 371-378, 1995 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:9yKSN-GCB0IC
Hydrophobic docking: a proposed enhancement to molecular recognition techniques IA Vakser, C Aflalo Proteins: Structure, Function, and Bioinformatics 20 (4), 320-329, 1994 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:qjMakFHDy7sC
Templates are available to model nearly all complexes of structurally characterized proteins PJ Kundrotas, Z Zhu, J Janin, IA Vakser Proceedings of the National Academy of Sciences 109 (24), 9438-9441, 2012 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:e5wmG9Sq2KIC
A systematic study of low-resolution recognition in protein–protein complexes IA Vakser, OG Matar, CF Lam Proceedings of the National Academy of Sciences 96 (15), 8477-8482, 1999 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:UeHWp8X0CEIC
Development and testing of an automated approach to protein docking A Tovchigrechko, IA Vakser Proteins: Structure, Function, and Bioinformatics 60 (2), 296-301, 2005 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:WF5omc3nYNoC
Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: a CASP‐CAPRI experiment MF Lensink, S Velankar, A Kryshtafovych, SY Huang, … Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:SeFeTyx0c_EC
Evaluation of GRAMM low‐resolution docking methodology on the hemagglutinin‐antibody complex IA Vakser Proteins: Structure, Function, and Bioinformatics 29 (S1), 226-230, 1997 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:Tyk-4Ss8FVUC
Low‐resolution docking: prediction of complexes for underdetermined structures IA Vakser Biopolymers 39 (3), 455-464, 1996 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:zYLM7Y9cAGgC
Docking of protein models A Tovchigrechko, CA Wells, IA Vakser Protein Science 11 (8), 1888-1896, 2002 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:Y0pCki6q_DkC
Blind prediction of homo‐and hetero‐protein complexes: The CASP13‐CAPRI experiment MF Lensink, G Brysbaert, N Nadzirin, S Velankar, RAG Chaleil, T Gerguri, … Proteins: Structure, Function, and Bioinformatics 87 (12), 1200-1221, 2019 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:sSrBHYA8nusC
How common is the funnel‐like energy landscape in protein‐protein interactions? A Tovchigrechko, IA Vakser Protein science 10 (8), 1572-1583, 2001 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:eQOLeE2rZwMC
Dockground resource for studying protein–protein interfaces D Douguet, HC Chen, A Tovchigrechko, IA Vakser Bioinformatics 22 (21), 2612-2618, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:_FxGoFyzp5QC
Docking by structural similarity at protein‐protein interfaces R Sinha, PJ Kundrotas, IA Vakser Proteins: Structure, Function, and Bioinformatics 78 (15), 3235-3241, 2010 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:Zph67rFs4hoC
Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction IA Vakser Protein Engineering, Design and Selection 9 (1), 37-41, 1996 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=4rSlPOIAAAAJ&citationforview=4rSlPOIAAAAJ:YsMSGLbcyi4C
Petras Kundrotas googlescholarauthorid petraskundrotas.md:JvYJSc4AAAAJ
Andrey Tovchigrechko googlescholarauthorid andreytovchigrechko.md:ULtDvKYAAAAJ
Ivan Anishchenko googlescholarauthorid ivananishchenko.md:Hp8zwAgAAAAJ
Alexander Tuzikov googlescholarauthorid alexandertuzikov.md:EL7ilZEAAAAJ
Anatoly M. Ruvinsky googlescholarauthorid anatolym._ruvinsky.md:09ZOiRYAAAAJ
Joel Janin googlescholarauthorid joeljanin.md:R71twNgAAAAJ
M Sternberg googlescholarauthorid msternberg.md:TDuw5O0AAAAJ
Claude Aflalo googlescholarauthorid claudeaflalo.md:AX2nYIwAAAAJ
Sandor Vajda googlescholarauthorid sandorvajda.md:_gYtig8AAAAJ
Zhengwei Zhu googlescholarauthorid zhengweizhu.md:Y54z02YAAAAJ