| Year |
Citation |
Score |
| 2023 |
Singh A, Copeland MM, Kundrotas PJ, Vakser IA. GRAMM Web Server for Protein Docking. Methods in Molecular Biology (Clifton, N.J.). 2714: 101-112. PMID 37676594 DOI: 10.1007/978-1-0716-3441-7_5 |
0.538 |
|
| 2023 |
Vakser IA. Prediction of protein interactions is essential for studying biomolecular mechanisms. Proteomics. 23: e2300219. PMID 37667816 DOI: 10.1002/pmic.202300219 |
0.571 |
|
| 2022 |
Chen SJ, Hassan M, Jernigan RL, Jia K, Kihara D, Kloczkowski A, Kotelnikov S, Kozakov D, Liang J, Liwo A, Matysiak S, Meller J, Micheletti C, Mitchell JC, Mondal S, ... ... Vakser I, et al. Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proceedings of the National Academy of Sciences of the United States of America. 120: e2214423119. PMID 36580595 DOI: 10.1073/pnas.2214423119 |
0.472 |
|
| 2022 |
Jenkins NW, Kundrotas PJ, Vakser IA. Size of the protein-protein energy funnel in crowded environment. Frontiers in Molecular Biosciences. 9: 1031225. PMID 36425657 DOI: 10.3389/fmolb.2022.1031225 |
0.496 |
|
| 2022 |
Collins KW, Copeland MM, Kotthoff I, Singh A, Kundrotas PJ, Vakser IA. DOCKGROUND resource for protein recognition studies. Protein Science : a Publication of the Protein Society. e4481. PMID 36281025 DOI: 10.1002/pro.4481 |
0.636 |
|
| 2022 |
Vakser IA, Grudinin S, Jenkins NW, Kundrotas PJ, Deeds EJ. Docking-based long timescale simulation of cell-size protein systems at atomic resolution. Proceedings of the National Academy of Sciences of the United States of America. 119: e2210249119. PMID 36191203 DOI: 10.1073/pnas.2210249119 |
0.418 |
|
| 2022 |
Malladi S, Powell HR, David A, Islam SA, Copeland MM, Kundrotas PJ, Sternberg MJE, Vakser IA. GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes. Journal of Molecular Biology. 434: 167608. PMID 35662458 DOI: 10.1016/j.jmb.2022.167608 |
0.636 |
|
| 2022 |
Kotthoff I, Kundrotas PJ, Vakser IA. DOCKGROUND membrane protein-protein set. Plos One. 17: e0267531. PMID 35580077 DOI: 10.1371/journal.pone.0267531 |
0.518 |
|
| 2022 |
Kotthoff I, Kundrotas PJ, Vakser IA. Dockground scoring benchmarks for protein docking. Proteins. PMID 35072956 DOI: 10.1002/prot.26306 |
0.574 |
|
| 2021 |
Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, ... ... Vakser IA, et al. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins. PMID 34453465 DOI: 10.1002/prot.26222 |
0.348 |
|
| 2020 |
Hadarovich A, Chakravarty D, Tuzikov AV, Ben-Tal N, Kundrotas PJ, Vakser IA. Structural motifs in protein cores and at protein-protein interfaces are different. Protein Science : a Publication of the Protein Society. PMID 33166001 DOI: 10.1002/pro.3996 |
0.636 |
|
| 2020 |
Badal VD, Kundrotas PJ, Vakser IA. Text mining for modeling of protein complexes enhanced by machine learning. Bioinformatics (Oxford, England). PMID 32960948 DOI: 10.1093/bioinformatics/btaa823 |
0.614 |
|
| 2020 |
Vakser IA. Challenges in protein docking. Current Opinion in Structural Biology. 64: 160-165. PMID 32836051 DOI: 10.1016/j.sbi.2020.07.001 |
0.57 |
|
| 2020 |
Kundrotas PJ, Kotthoff I, Choi SW, Copeland MM, Vakser IA. Dockground Tool for Development and Benchmarking of Protein Docking Procedures. Methods in Molecular Biology (Clifton, N.J.). 2165: 289-300. PMID 32621232 DOI: 10.1007/978-1-0716-0708-4_17 |
0.578 |
|
| 2020 |
Singh A, Dauzhenka T, Kundrotas PJ, Sternberg MJE, Vakser IA. Application of docking methodologies to modeled proteins. Proteins. PMID 32170770 DOI: 10.1002/prot.25889 |
0.642 |
|
| 2020 |
Chakravarty D, McElfresh GW, Kundrotas PJ, Vakser IA. How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking. Proteins. PMID 31994759 DOI: 10.1002/prot.25875 |
0.643 |
|
| 2020 |
Hadarovich AY, Anishchenko IV, Kundrotas P, Vakser I, Tuzikov AV. Structure prediction algorithm for protein complexes based on gene ontology Doklady of the National Academy of Sciences of Belarus. 64: 150-158. DOI: 10.29235/1561-8323-2020-64-2-150-158 |
0.553 |
|
| 2020 |
Dauzhenka T, Anishchenko I, Kundrotas P, Vakser I. Protein Docking Refinement with Systematic Conformational Search - Application to Models Inside the Docking Funnel Biophysical Journal. 118: 516a. DOI: 10.1016/J.Bpj.2019.11.2841 |
0.56 |
|
| 2020 |
Singh A, Dauzhenka T, Kundrotas P, Sternberg MJ, Vakser I. Application of Docking to Protein Models Biophysical Journal. 118: 360a. DOI: 10.1016/J.Bpj.2019.11.2072 |
0.552 |
|
| 2020 |
Kotthoff IP, Kundrotas PJ, Vakser IA. Docking Decoys for Modeled Proteins Biophysical Journal. 118: 306a. DOI: 10.1016/j.bpj.2019.11.1729 |
0.534 |
|
| 2019 |
Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, ... ... Vakser IA, et al. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins. PMID 31612567 DOI: 10.1002/Prot.25838 |
0.429 |
|
| 2019 |
Ofoegbu TC, David A, Kelley LA, Mezulis S, Islam SA, Mersmann SF, Strömich L, Vakser IA, Houlston RS, Sternberg MJE. PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants. Journal of Molecular Biology. PMID 31075275 DOI: 10.1016/j.jmb.2019.04.043 |
0.516 |
|
| 2019 |
Vakser IA, Deeds EJ. Computational approaches to macromolecular interactions in the cell. Current Opinion in Structural Biology. 55: 59-65. PMID 30999240 DOI: 10.1016/J.Sbi.2019.03.012 |
0.315 |
|
| 2018 |
Hadarovich A, Anishchenko I, Tuzikov AV, Kundrotas PJ, Vakser IA. Gene ontology improves template selection in comparative protein docking. Proteins. PMID 30520123 DOI: 10.1002/prot.25645 |
0.633 |
|
| 2018 |
Dauzhenka T, Kundrotas PJ, Vakser IA. Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking. Journal of Computational Chemistry. PMID 30226647 DOI: 10.1002/jcc.25381 |
0.476 |
|
| 2018 |
Anishchenko I, Kundrotas PJ, Vakser IA. Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model. Biophysical Journal. 115: 809-821. PMID 30122295 DOI: 10.1016/j.bpj.2018.07.035 |
0.581 |
|
| 2018 |
Belkin S, Kundrotas PJ, Vakser IA. Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking. Journal of Computer-Aided Molecular Design. PMID 30003468 DOI: 10.1007/s10822-018-0124-z |
0.557 |
|
| 2018 |
Badal VD, Kundrotas PJ, Vakser IA. Natural language processing in text mining for structural modeling of protein complexes. Bmc Bioinformatics. 19: 84. PMID 29506465 DOI: 10.1186/s12859-018-2079-4 |
0.538 |
|
| 2018 |
Dauzhenka T, Anishchenko I, Kundrotas PJ, Vakser IA. Relative Contribution of the Refinement Steps to the Protein-Protein Docking Success Rate Biophysical Journal. 114: 575a. DOI: 10.1016/j.bpj.2017.11.3147 |
0.489 |
|
| 2018 |
Kundrotas P, Belkin S, Vakser I. Structure-Function Relationships in Protein Complexes Biophysical Journal. 114: 46a. DOI: 10.1016/J.Bpj.2017.11.303 |
0.568 |
|
| 2017 |
Kundrotas PJ, Anishchenko I, Badal VD, Das M, Dauzhenka T, Vakser IA. Modeling CAPRI Targets 110 - 120 by Template-Based and Free Docking Using Contact Potential and Combined Scoring Function. Proteins. PMID 28905425 DOI: 10.1002/Prot.25380 |
0.371 |
|
| 2017 |
Kundrotas PJ, Anishchenko I, Dauzhenka T, Kotthoff I, Mnevets D, Copeland MM, Vakser IA. Dockground: A comprehensive data resource for modeling of protein complexes. Protein Science : a Publication of the Protein Society. PMID 28891124 DOI: 10.1002/pro.3295 |
0.662 |
|
| 2016 |
Anishchenko I, Kundrotas PJ, Vakser IA. Structural quality of unrefined models in protein docking. Proteins. PMID 27756103 DOI: 10.1002/prot.25188 |
0.657 |
|
| 2016 |
Anishchenko I, Kundrotas PJ, Vakser IA. Modeling Complexes of Modeled Proteins. Proteins. PMID 27701777 DOI: 10.1002/prot.25183 |
0.657 |
|
| 2016 |
Zheng J, Kundrotas PJ, Vakser IA, Liu S. Template-Based Modeling of Protein-RNA Interactions. Plos Computational Biology. 12: e1005120. PMID 27662342 DOI: 10.1371/journal.pcbi.1005120 |
0.448 |
|
| 2016 |
Im W, Liang J, Olson A, Zhou HX, Vajda S, Vakser IA. Challenges in structural approaches to cell modeling. Journal of Molecular Biology. PMID 27255863 DOI: 10.1016/J.Jmb.2016.05.024 |
0.419 |
|
| 2016 |
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, ... ... Vakser IA, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007 |
0.532 |
|
| 2015 |
Badal VD, Kundrotas PJ, Vakser IA. Text Mining for Protein Docking. Plos Computational Biology. 11: e1004630. PMID 26650466 DOI: 10.1371/journal.pcbi.1004630 |
0.595 |
|
| 2015 |
Kirys T, Ruvinsky AM, Singla D, Tuzikov AV, Kundrotas PJ, Vakser IA. Simulated unbound structures for benchmarking of protein docking in the DOCKGROUND resource. Bmc Bioinformatics. 16: 243. PMID 26227548 DOI: 10.1186/s12859-015-0672-3 |
0.593 |
|
| 2015 |
Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA. Protein models docking benchmark 2. Proteins. 83: 891-7. PMID 25712716 DOI: 10.1002/prot.24784 |
0.618 |
|
| 2015 |
Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA. Structural templates for comparative protein docking. Proteins. 83: 1563-70. PMID 25488330 DOI: 10.1002/prot.24736 |
0.653 |
|
| 2014 |
Vakser IA. Protein-protein docking: from interaction to interactome. Biophysical Journal. 107: 1785-93. PMID 25418159 DOI: 10.1016/j.bpj.2014.08.033 |
0.665 |
|
| 2014 |
Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, ... ... Vakser IA, et al. Blind prediction of interfacial water positions in CAPRI. Proteins. 82: 620-32. PMID 24155158 DOI: 10.1002/Prot.24439 |
0.359 |
|
| 2014 |
Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA. Protein models: the Grand Challenge of protein docking. Proteins. 82: 278-87. PMID 23934791 DOI: 10.1002/prot.24385 |
0.645 |
|
| 2014 |
Kundrotas P, Vakser I, Janin J. Structural Similarity in Modeling of Homodimers Biophysical Journal. 106: 656a. DOI: 10.1016/J.Bpj.2013.11.3630 |
0.574 |
|
| 2013 |
Kundrotas PJ, Vakser IA, Janin J. Structural templates for modeling homodimers. Protein Science : a Publication of the Protein Society. 22: 1655-63. PMID 23996787 DOI: 10.1002/Pro.2361 |
0.615 |
|
| 2013 |
Kundrotas PJ, Vakser IA. Global and local structural similarity in protein-protein complexes: implications for template-based docking. Proteins. 81: 2137-42. PMID 23946125 DOI: 10.1002/prot.24392 |
0.685 |
|
| 2013 |
Kundrotas PJ, Vakser IA. Protein-protein alternative binding modes do not overlap. Protein Science : a Publication of the Protein Society. 22: 1141-5. PMID 23775945 DOI: 10.1002/pro.2295 |
0.528 |
|
| 2013 |
Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA. Ensemble-based characterization of unbound and bound states on protein energy landscape. Protein Science : a Publication of the Protein Society. 22: 734-44. PMID 23526684 DOI: 10.1002/pro.2256 |
0.334 |
|
| 2013 |
Vakser IA. Low-resolution structural modeling of protein interactome. Current Opinion in Structural Biology. 23: 198-205. PMID 23294579 DOI: 10.1016/j.sbi.2012.12.003 |
0.64 |
|
| 2012 |
Kundrotas PJ, Zhu Z, Vakser IA. GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions. Human Genomics. 6: 7. PMID 23245398 DOI: 10.1186/1479-7364-6-7 |
0.576 |
|
| 2012 |
Kirys T, Ruvinsky AM, Tuzikov AV, Vakser IA. Correlation analysis of the side-chains conformational distribution in bound and unbound proteins. Bmc Bioinformatics. 13: 236. PMID 22984947 DOI: 10.1186/1471-2105-13-236 |
0.568 |
|
| 2012 |
Yao H, Wang Y, Lovell S, Kumar R, Ruvinsky AM, Battaile KP, Vakser IA, Rivera M. The structure of the BfrB-Bfd complex reveals protein-protein interactions enabling iron release from bacterioferritin. Journal of the American Chemical Society. 134: 13470-81. PMID 22812654 DOI: 10.1021/Ja305180N |
0.322 |
|
| 2012 |
Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA. Structure fluctuations and conformational changes in protein binding. Journal of Bioinformatics and Computational Biology. 10: 1241002. PMID 22809338 DOI: 10.1142/S0219720012410028 |
0.452 |
|
| 2012 |
Kundrotas PJ, Zhu Z, Janin J, Vakser IA. Templates are available to model nearly all complexes of structurally characterized proteins. Proceedings of the National Academy of Sciences of the United States of America. 109: 9438-41. PMID 22645367 DOI: 10.1073/pnas.1200678109 |
0.676 |
|
| 2012 |
Sinha R, Kundrotas PJ, Vakser IA. Protein docking by the interface structure similarity: how much structure is needed? Plos One. 7: e31349. PMID 22348074 DOI: 10.1371/Journal.Pone.0031349 |
0.621 |
|
| 2011 |
Liu S, Vakser IA. DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking. Bmc Bioinformatics. 12: 280. PMID 21745398 DOI: 10.1186/1471-2105-12-280 |
0.546 |
|
| 2011 |
Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA. Side-chain conformational changes upon Protein-Protein Association. Journal of Molecular Biology. 408: 356-65. PMID 21354429 DOI: 10.1016/j.jmb.2011.02.030 |
0.369 |
|
| 2011 |
Ruvinsky AM, Kirus T, Tuzikov AV, Vakser IA. Structural Fluctuations and Conformational Changes in Proteins and Protein Complexes Biophysical Journal. 100: 372a. DOI: 10.1016/j.bpj.2010.12.2215 |
0.587 |
|
| 2011 |
Kundrotas PJ, Anishchenko I, Tuzikov AV, Vakser I. Docking Benchmark Set of Protein Models Biophysical Journal. 100: 320a. DOI: 10.1016/j.bpj.2010.12.1947 |
0.479 |
|
| 2010 |
Ruvinsky AM, Vakser IA. Sequence composition and environment effects on residue fluctuations in protein structures. The Journal of Chemical Physics. 133: 155101. PMID 20969427 DOI: 10.1063/1.3498743 |
0.51 |
|
| 2010 |
Sinha R, Kundrotas PJ, Vakser IA. Docking by structural similarity at protein-protein interfaces. Proteins. 78: 3235-41. PMID 20715056 DOI: 10.1016/J.Bpj.2009.12.1043 |
0.626 |
|
| 2010 |
Kundrotas PJ, Vakser IA. Accuracy of protein-protein binding sites in high-throughput template-based modeling. Plos Computational Biology. 6: e1000727. PMID 20369011 DOI: 10.1371/journal.pcbi.1000727 |
0.615 |
|
| 2010 |
Kundrotas PJ, Zhu Z, Vakser IA. GWIDD: Genome-wide protein docking database. Nucleic Acids Research. 38: D513-7. PMID 19900970 DOI: 10.1093/nar/gkp944 |
0.431 |
|
| 2010 |
Ruvinsky AM, Vakser IA. Structure Fluctuations in Proteins and their Relationship to Amino Acid Propensities Biophysical Journal. 98: 225a. DOI: 10.1016/j.bpj.2009.12.1219 |
0.391 |
|
| 2009 |
Ruvinsky AM, Vakser IA. The ruggedness of protein-protein energy landscape and the cutoff for 1/r(n) potentials. Bioinformatics (Oxford, England). 25: 1132-6. PMID 19237445 DOI: 10.1093/bioinformatics/btp108 |
0.488 |
|
| 2009 |
Kundrotas P, Vakser IA. Template-Based Modeling of Protein-Protein Interfaces Biophysical Journal. 96: 652a. DOI: 10.1016/j.bpj.2008.12.3445 |
0.568 |
|
| 2008 |
Liu S, Gao Y, Vakser IA. DOCKGROUND protein-protein docking decoy set. Bioinformatics (Oxford, England). 24: 2634-5. PMID 18812365 DOI: 10.1093/bioinformatics/btn497 |
0.521 |
|
| 2008 |
Zhu Z, Tovchigrechko A, Baronova T, Gao Y, Douguet D, O'Toole N, Vakser IA. Large-scale structural modeling of protein complexes at low resolution. Journal of Bioinformatics and Computational Biology. 6: 789-810. PMID 18763743 DOI: 10.1142/S0219720008003679 |
0.637 |
|
| 2008 |
Ruvinsky AM, Vakser IA. Chasing funnels on protein-protein energy landscapes at different resolutions. Biophysical Journal. 95: 2150-9. PMID 18515374 DOI: 10.1529/biophysj.108.132977 |
0.417 |
|
| 2008 |
Vakser IA, Kundrotas P. Predicting 3D structures of protein-protein complexes. Current Pharmaceutical Biotechnology. 9: 57-66. PMID 18393862 DOI: 10.2174/138920108783955209 |
0.642 |
|
| 2008 |
Hunjan J, Tovchigrechko A, Gao Y, Vakser IA. The size of the intermolecular energy funnel in protein-protein interactions. Proteins. 72: 344-52. PMID 18214966 DOI: 10.1002/prot.21930 |
0.417 |
|
| 2008 |
Vakser IA. PSI has to live and become PCI: Protein Complex Initiative. Structure (London, England : 1993). 16: 1-3. PMID 18184573 DOI: 10.1016/j.str.2007.12.005 |
0.452 |
|
| 2008 |
O'Toole N, Vakser IA. Large-scale characteristics of the energy landscape in protein-protein interactions. Proteins. 71: 144-52. PMID 17932937 DOI: 10.1002/prot.21665 |
0.479 |
|
| 2008 |
Ruvinsky AM, Vakser IA. Interaction cutoff effect on ruggedness of protein-protein energy landscape. Proteins. 70: 1498-505. PMID 17910068 DOI: 10.1002/prot.21644 |
0.426 |
|
| 2007 |
Gao Y, Douguet D, Tovchigrechko A, Vakser IA. DOCKGROUND system of databases for protein recognition studies: unbound structures for docking. Proteins. 69: 845-51. PMID 17803215 DOI: 10.1002/prot.21714 |
0.577 |
|
| 2007 |
Nicola G, Vakser IA. A simple shape characteristic of protein-protein recognition. Bioinformatics (Oxford, England). 23: 789-92. PMID 17267427 DOI: 10.1093/bioinformatics/btm018 |
0.544 |
|
| 2006 |
Douguet D, Chen HC, Tovchigrechko A, Vakser IA. DOCKGROUND resource for studying protein-protein interfaces. Bioinformatics (Oxford, England). 22: 2612-8. PMID 16928732 DOI: 10.1093/bioinformatics/btl447 |
0.538 |
|
| 2006 |
Tovchigrechko A, Vakser IA. GRAMM-X public web server for protein-protein docking. Nucleic Acids Research. 34: W310-4. PMID 16845016 DOI: 10.1093/nar/gkl206 |
0.366 |
|
| 2005 |
Tovchigrechko A, Vakser IA. Development and testing of an automated approach to protein docking. Proteins. 60: 296-301. PMID 15981259 DOI: 10.1002/prot.20573 |
0.425 |
|
| 2004 |
Vakser IA. Protein-protein interfaces are special. Structure (London, England : 1993). 12: 910-2. PMID 15274910 DOI: 10.1016/j.str.2004.05.003 |
0.523 |
|
| 2004 |
Jiang S, Vakser IA. Shorter side chains optimize helix-helix packing. Protein Science : a Publication of the Protein Society. 13: 1426-9. PMID 15075402 DOI: 10.1110/ps.03505804 |
0.482 |
|
| 2003 |
Jiang S, Tovchigrechko A, Vakser IA. The role of geometric complementarity in secondary structure packing: a systematic docking study. Protein Science : a Publication of the Protein Society. 12: 1646-51. PMID 12876314 DOI: 10.1110/ps.0304503 |
0.521 |
|
| 2003 |
Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ. CAPRI: a Critical Assessment of PRedicted Interactions. Proteins. 52: 2-9. PMID 12784359 DOI: 10.1002/Prot.10381 |
0.614 |
|
| 2002 |
Tovchigrechko A, Wells CA, Vakser IA. Docking of protein models. Protein Science : a Publication of the Protein Society. 11: 1888-96. PMID 12142443 DOI: 10.1110/ps.4730102 |
0.669 |
|
| 2002 |
Vajda S, Vakser IA, Sternberg MJ, Janin J. Modeling of protein interactions in genomes. Proteins. 47: 444-6. PMID 12001222 DOI: 10.1002/Prot.10112 |
0.369 |
|
| 2002 |
Vakser IA, Jiang S. Strategies for modeling the interactions of transmembrane helices of G protein-coupled receptors by geometric complementarity using the GRAMM computer algorithm. Methods in Enzymology. 343: 313-28. PMID 11665577 DOI: 10.1016/S0076-6879(02)43144-8 |
0.321 |
|
| 2001 |
Tovchigrechko A, Vakser IA. How common is the funnel-like energy landscape in protein-protein interactions? Protein Science. 10: 1572-1583. PMID 11468354 DOI: 10.1110/ps.8701 |
0.502 |
|
| 2001 |
Glaser F, Steinberg DM, Vakser IA, Ben-Tal N. Residue frequencies and pairing preferences at protein-protein interfaces. Proteins. 43: 89-102. PMID 11276079 DOI: 10.1002/1097-0134(20010501)43:2<89::Aid-Prot1021>3.0.Co;2-H |
0.378 |
|
| 1999 |
Vakser IA, Matar OG, Lam CF. A systematic study of low-resolution recognition in protein-protein complexes Proceedings of the National Academy of Sciences of the United States of America. 96: 8477-8482. PMID 10411900 DOI: 10.1073/pnas.96.15.8477 |
0.479 |
|
| 1997 |
Vakser IA. Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex Proteins: Structure, Function and Genetics. 29: 226-230. PMID 9485517 DOI: 10.1002/(SICI)1097-0134(1997)1+<226::AID-PROT31>3.0.CO;2-O |
0.465 |
|
| 1996 |
Vakser IA. Main-chain complementarity in protein-protein recognition Protein Engineering. 9: 741-744. PMID 8888139 |
0.417 |
|
| 1996 |
Vakser IA. Low-resolution docking: Prediction of complexes for underdetermined structures Biopolymers. 39: 455-464. PMID 8756522 DOI: 10.1002/(SICI)1097-0282(199609)39:3<455::AID-BIP16>3.0.CO;2-A |
0.427 |
|
| 1996 |
Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. The Role of Geometric Fit Between Protein Molecules and their Ligands in Determining Biological Specificity Advances in Molecular and Cell Biology. 15: 623-637. DOI: 10.1016/S1569-2558(08)60142-3 |
0.413 |
|
| 1995 |
Vakser IA. Protein docking for low-resolution structures Protein Engineering. 8: 371-377. PMID 7567922 |
0.463 |
|
| Show low-probability matches. |