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ORCIDIlya A. Vakser
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2020 – today
- 2021
[j20]Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser:
Text mining for modeling of protein complexes enhanced by machine learning. Bioinform. 37(4): 497-505 (2021)
2010 – 2019
- 2018
- [j19]Varsha D. Badal
, Petras J. Kundrotas, Ilya A. Vakser:
Natural language processing in text mining for structural modeling of protein complexes. BMC Bioinform. 19(1): 84:1-84:10 (2018) - [j18]Saveliy Belkin, Petras J. Kundrotas, Ilya A. Vakser:
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(7): 769-779 (2018) - [j17]Taras Dauzhenka, Petras J. Kundrotas, Ilya A. Vakser:
Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking. J. Comput. Chem. 39(24): 2012-2021 (2018) - 2017
- [j16]Ruth Nussinov, Jason A. Papin, Ilya A. Vakser:
Computing the Dynamic Supramolecular Structural Proteome. PLoS Comput. Biol. 13(1) (2017) - 2016
- [j15]Jinfang Zheng, Petras J. Kundrotas, Ilya A. Vakser, Shiyong Liu:
Template-Based Modeling of Protein-RNA Interactions. PLoS Comput. Biol. 12(9) (2016) - [c1]Ivan V. Anishchenko, Varsha D. Badal, Taras Dauzhenka, Madhurima Das, Alexander V. Tuzikov, Petras J. Kundrotas, Ilya A. Vakser:
Genome-Wide Structural Modeling of Protein-Protein Interactions. ISBRA 2016: 95-105 - 2015
- [j14]Tatsiana Kirys, Anatoly M. Ruvinsky, Deepak Singla, Alexander V. Tuzikov, Petras J. Kundrotas, Ilya A. Vakser:
Simulated unbound structures for benchmarking of protein docking in the Dockground resource. BMC Bioinform. 16: 243:1-243:6 (2015) - [j13]Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser:
Text Mining for Protein Docking. PLoS Comput. Biol. 11(12) (2015) - 2012
- [j12]Tatsiana Kirys, Anatoly M. Ruvinsky, Alexander V. Tuzikov, Ilya A. Vakser:
Correlation analysis of the side-chains conformational distribution in bound and unbound proteins. BMC Bioinform. 13: 236 (2012) - [j11]Anatoly M. Ruvinsky, Tatsiana Kirys, Alexander V. Tuzikov, Ilya A. Vakser:
Structure fluctuations and conformational Changes in protein binding. J. Bioinform. Comput. Biol. 10(2) (2012) - 2011
- [j10]Shiyong Liu, Ilya A. Vakser:
DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking. BMC Bioinform. 12: 280 (2011) - 2010
- [j9]Petras J. Kundrotas, Zhengwei Zhu, Ilya A. Vakser:
GWIDD: Genome-wide protein docking database. Nucleic Acids Res. 38(Database-Issue): 513-517 (2010) - [j8]Petras J. Kundrotas, Ilya A. Vakser:
Accuracy of Protein-Protein Binding Sites in High-Throughput Template-Based Modeling. PLoS Comput. Biol. 6(4) (2010)
2000 – 2009
- 2009
- [j7]Anatoly M. Ruvinsky, Ilya A. Vakser:
The ruggedness of protein-protein energy landscape and the cutoff for 1/rn potentials. Bioinform. 25(9): 1132-1136 (2009) - 2008
- [j6]Shiyong Liu, Ying Gao, Ilya A. Vakser:
DOCKGROUND protein-protein docking decoy set. Bioinform. 24(22): 2634-2635 (2008) - [j5]Zhengwei Zhu, Andrey Tovchigrechko, Tatiana Baronova, Ying Gao, Dominique Douguet, Nicholas O'Toole, Ilya A. Vakser:
Large-Scale Structural Modeling of protein complexes at Low Resolution. J. Bioinform. Comput. Biol. 6(4): 789-810 (2008) - 2007
- [j4]George Nicola, Ilya A. Vakser:
A simple shape characteristic of protein-protein recognition. Bioinform. 23(7): 789-792 (2007) - [j3]George Nicola, Ilya A. Vakser:
A simple shape characteristic of protein-protein recognition. Bioinform. 23(16): 2201 (2007) - 2006
- [j2]Dominique Douguet, Huei-Chi Chen, Andrey Tovchigrechko, Ilya A. Vakser:
DOCKGROUND resource for studying protein-protein interfaces. Bioinform. 22(21): 2612-2618 (2006) - [j1]Andrey Tovchigrechko, Ilya A. Vakser:
GRAMM-X public web server for protein-protein docking. Nucleic Acids Res. 34(Web-Server-Issue): 310-314 (2006)
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