Ilya A. Vakser

According to our database, Ilya A. Vakser authored at least 20 papers between 2006 and 2021.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2021

Text mining for modeling of protein complexes enhanced by machine learning.

Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser

Bioinform., 2021

2018

Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking.

Taras Dauzhenka, Petras J. Kundrotas, Ilya A. Vakser

J. Comput. Chem., 2018

Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking.

Saveliy Belkin, Petras J. Kundrotas, Ilya A. Vakser

J. Comput. Aided Mol. Des., 2018

Natural language processing in text mining for structural modeling of protein complexes.

Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser

BMC Bioinform., 2018

2017

Computing the Dynamic Supramolecular Structural Proteome.

Ruth Nussinov, Jason A. Papin, Ilya A. Vakser

PLoS Comput. Biol., 2017

2016

Template-Based Modeling of Protein-RNA Interactions.

Jinfang Zheng, Petras J. Kundrotas, Ilya A. Vakser, Shiyong Liu

PLoS Comput. Biol., 2016

Genome-Wide Structural Modeling of Protein-Protein Interactions.

Ivan V. Anishchenko, Varsha D. Badal, Taras Dauzhenka, Madhurima Das, Alexander V. Tuzikov, Petras J. Kundrotas, Ilya A. Vakser

Proceedings of the Bioinformatics Research and Applications - 12th International Symposium, 2016

2015

Text Mining for Protein Docking.

Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser

PLoS Comput. Biol., 2015

Simulated unbound structures for benchmarking of protein docking in the Dockground resource.

Tatsiana Kirys, Anatoly M. Ruvinsky, Deepak Singla, Alexander V. Tuzikov, Petras J. Kundrotas, Ilya A. Vakser

BMC Bioinform., 2015

2012

Structure fluctuations and conformational Changes in protein binding.

Anatoly M. Ruvinsky, Tatsiana Kirys, Alexander V. Tuzikov, Ilya A. Vakser

J. Bioinform. Comput. Biol., 2012

Correlation analysis of the side-chains conformational distribution in bound and unbound proteins.

Tatsiana Kirys, Anatoly M. Ruvinsky, Alexander V. Tuzikov, Ilya A. Vakser

BMC Bioinform., 2012

2011

DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking.

Shiyong Liu, Ilya A. Vakser

BMC Bioinform., 2011

2010

Accuracy of Protein-Protein Binding Sites in High-Throughput Template-Based Modeling.

Petras J. Kundrotas, Ilya A. Vakser

PLoS Comput. Biol., 2010

GWIDD: Genome-wide protein docking database.

Petras J. Kundrotas, Zhengwei Zhu, Ilya A. Vakser

Nucleic Acids Res., 2010

2009

The ruggedness of protein-protein energy landscape and the cutoff for 1/<i>r</i>^<i>n</i> potentials.

Anatoly M. Ruvinsky, Ilya A. Vakser

Bioinform., 2009

2008

Large-Scale Structural Modeling of protein complexes at Low Resolution.

Zhengwei Zhu, Andrey Tovchigrechko, Tatiana Baronova, Ying Gao, Dominique Douguet, Nicholas O'Toole, Ilya A. Vakser

J. Bioinform. Comput. Biol., 2008

DOCKGROUND protein-protein docking decoy set.

Shiyong Liu, Ying Gao, Ilya A. Vakser

Bioinform., 2008

2007

A simple shape characteristic of protein-protein recognition.

George Nicola, Ilya A. Vakser

Bioinform., 2007

2006

GRAMM-X public web server for protein-protein docking.

Andrey Tovchigrechko, Ilya A. Vakser

Nucleic Acids Res., 2006

DOCKGROUND resource for studying protein-protein interfaces.

Dominique Douguet, Huei-Chi Chen, Andrey Tovchigrechko, Ilya A. Vakser

Bioinform., 2006