Ilya A. Vakser

21 papers Journal 20Unranked 1
YearRankTypeTitle / Venue / Authors
2021 J jnl
Text mining for modeling of protein complexes enhanced by machine learning.
Bioinform.
Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser
2018 J jnl
Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking.
J. Comput. Chem.
Taras Dauzhenka, Petras J. Kundrotas, Ilya A. Vakser
2018 J jnl
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.
Saveliy Belkin, Petras J. Kundrotas, Ilya A. Vakser
2018 J jnl
Natural language processing in text mining for structural modeling of protein complexes.
BMC Bioinform.
Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser
2017 J jnl
Computing the Dynamic Supramolecular Structural Proteome.
PLoS Comput. Biol.
Ruth Nussinov, Jason A. Papin, Ilya A. Vakser
2016 — conf
Genome-Wide Structural Modeling of Protein-Protein Interactions.
ISBRA
Ivan V. Anishchenko, Varsha D. Badal, Taras Dauzhenka, Madhurima Das, Alexander V. Tuzikov, Petras J. Kundrotas, Ilya A. Vakser
2016 J jnl
Template-Based Modeling of Protein-RNA Interactions.
PLoS Comput. Biol.
Jinfang Zheng, Petras J. Kundrotas, Ilya A. Vakser, Shiyong Liu
2015 J jnl
Simulated unbound structures for benchmarking of protein docking in the Dockground resource.
BMC Bioinform.
Tatsiana Kirys, Anatoly M. Ruvinsky, Deepak Singla, Alexander V. Tuzikov, Petras J. Kundrotas, Ilya A. Vakser
2015 J jnl
Text Mining for Protein Docking.
PLoS Comput. Biol.
Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser
2012 J jnl
Correlation analysis of the side-chains conformational distribution in bound and unbound proteins.
BMC Bioinform.
Tatsiana Kirys, Anatoly M. Ruvinsky, Alexander V. Tuzikov, Ilya A. Vakser
2012 J jnl
Structure fluctuations and conformational Changes in protein binding.
J. Bioinform. Comput. Biol.
Anatoly M. Ruvinsky, Tatsiana Kirys, Alexander V. Tuzikov, Ilya A. Vakser
2011 J jnl
DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking.
BMC Bioinform.
Shiyong Liu, Ilya A. Vakser
2010 J jnl
Accuracy of Protein-Protein Binding Sites in High-Throughput Template-Based Modeling.
PLoS Comput. Biol.
Petras J. Kundrotas, Ilya A. Vakser
2010 J jnl
GWIDD: Genome-wide protein docking database.
Nucleic Acids Res.
Petras J. Kundrotas, Zhengwei Zhu, Ilya A. Vakser
2009 J jnl
The ruggedness of protein-protein energy landscape and the cutoff for 1/
Bioinform.
Anatoly M. Ruvinsky, Ilya A. Vakser
2008 J jnl
DOCKGROUND protein-protein docking decoy set.
Bioinform.
Shiyong Liu, Ying Gao, Ilya A. Vakser
2008 J jnl
Large-Scale Structural Modeling of protein complexes at Low Resolution.
J. Bioinform. Comput. Biol.
Zhengwei Zhu, Andrey Tovchigrechko, Tatiana Baronova, Ying Gao, Dominique Douguet, Nicholas O'Toole, Ilya A. Vakser
2007 J jnl
A simple shape characteristic of protein-protein recognition.
Bioinform.
George Nicola, Ilya A. Vakser
2007 J jnl
A simple shape characteristic of protein-protein recognition.
Bioinform.
George Nicola, Ilya A. Vakser
2006 J jnl
DOCKGROUND resource for studying protein-protein interfaces.
Bioinform.
Dominique Douguet, Huei-Chi Chen, Andrey Tovchigrechko, Ilya A. Vakser
2006 J jnl
GRAMM-X public web server for protein-protein docking.
Nucleic Acids Res.
Andrey Tovchigrechko, Ilya A. Vakser