Ilya A. Vakser

Publication Activity (10 Years)

Years Active: 2006-2021
Publications (10 Years): 7

Top Topics

Protein Interaction

Protein Complexes

Exhaustive Search

Top Venues

PLoS Comput. Biol.

J. Comput. Chem.

Publications

Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser
Text mining for modeling of protein complexes enhanced by machine learning. Bioinform. 37 (4) (2021)
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) (2018)
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) (2018)
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) (2018)
Ruth Nussinov, Jason A. Papin, Ilya A. Vakser
Computing the Dynamic Supramolecular Structural Proteome. PLoS Comput. Biol. 13 (1) (2017)
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)
Jinfang Zheng, Petras J. Kundrotas, Ilya A. Vakser, Shiyong Liu
Template-Based Modeling of Protein-RNA Interactions. PLoS Comput. Biol. 12 (9) (2016)
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 (2015)
Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser
Text Mining for Protein Docking. PLoS Comput. Biol. 11 (12) (2015)
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)
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 (2012)
Shiyong Liu, Ilya A. Vakser
DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking. BMC Bioinform. 12 (2011)
Petras J. Kundrotas, Ilya A. Vakser
Accuracy of Protein-Protein Binding Sites in High-Throughput Template-Based Modeling. PLoS Comput. Biol. 6 (4) (2010)
Petras J. Kundrotas, Zhengwei Zhu, Ilya A. Vakser
GWIDD: Genome-wide protein docking database. Nucleic Acids Res. 38 (Database-Issue) (2010)
Anatoly M. Ruvinsky, Ilya A. Vakser
potentials. Bioinform. 25 (9) (2009)
Shiyong Liu, Ying Gao, Ilya A. Vakser
DOCKGROUND protein-protein docking decoy set. Bioinform. 24 (22) (2008)
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) (2008)
George Nicola, Ilya A. Vakser
A simple shape characteristic of protein-protein recognition. Bioinform. 23 (16) (2007)
George Nicola, Ilya A. Vakser
A simple shape characteristic of protein-protein recognition. Bioinform. 23 (7) (2007)
Andrey Tovchigrechko, Ilya A. Vakser
GRAMM-X public web server for protein-protein docking. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Dominique Douguet, Huei-Chi Chen, Andrey Tovchigrechko, Ilya A. Vakser
DOCKGROUND resource for studying protein-protein interfaces. Bioinform. 22 (21) (2006)