Ilya A. Vakser

发表

DOCKGROUND resource for studying protein-protein interfaces

Dominique Douguet, Huei-Chi Chen, Andrey Tovchigrechko, 2006, Bioinform..

Genome-Wide Structural Modeling of Protein-Protein Interactions

Petras J. Kundrotas, Ilya A. Vakser, Alexander V. Tuzikov, 2016, ISBRA.

Structure prediction algorithm for protein complexes based on gene ontology

Petras J. Kundrotas, Ilya A. Vakser, Alexander V. Tuzikov, 2020, Doklady of the National Academy of Sciences of Belarus.

DOCKGROUND protein-protein docking decoy set

Ying Gao, Ilya A. Vakser, Shiyong Liu, 2008, Bioinform..

Template-Based Modeling of Protein-RNA Interactions

Petras J. Kundrotas, Ilya A. Vakser, Shiyong Liu, 2016, PLoS Comput. Biol..

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

Ilya A. Vakser, Shiyong Liu, I. Vakser, 2011, BMC Bioinformatics.

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

Ilya A. Vakser, Alexander V. Tuzikov, Tatsiana Kirys, 2012, BMC Bioinformatics.

Modeling CAPRI targets 110‐120 by template‐based and free docking using contact potential and combined scoring function

Petras J. Kundrotas, Ilya A. Vakser, Varsha D. Badal, 2018, Proteins.

Text Mining for Protein Docking

Petras J. Kundrotas, Ilya A. Vakser, Varsha D. Badal, 2015, PLoS Comput. Biol..

Docking Benchmark Set of Protein Models

Petras J. Kundrotas, Ilya A. Vakser, Alexander V. Tuzikov, 2011 .

Large-Scale Structural Modeling of protein complexes at Low Resolution

Ying Gao, Dominique Douguet, Andrey Tovchigrechko, 2008, J. Bioinform. Comput. Biol..

Structural bioinformatics DOCKGROUND Protein-Protein Docking Decoy Set

Shiyong Liu, Ilya A. Vakser, Ying Gao, 2008 .

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

Petras J. Kundrotas, Ilya A. Vakser, I. Vakser, 2010, PLoS Comput. Biol..

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

Petras J. Kundrotas, Ilya A. Vakser, Saveliy Belkin, 2018, Journal of Computer-Aided Molecular Design.

Structure fluctuations and conformational Changes in protein binding

Ilya A. Vakser, Alexander V. Tuzikov, Tatsiana Kirys, 2012, J. Bioinform. Comput. Biol..

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

Petras J. Kundrotas, Ilya A. Vakser, Varsha D. Badal, 2018, BMC Bioinformatics.

GRAMM-X public web server for protein–protein docking

Andrey Tovchigrechko, Ilya A. Vakser, I. Vakser, 2006, Nucleic Acids Res..

Docking by Structural Similarity at Protein-Protein Interfaces

Petras J. Kundrotas, Ilya A. Vakser, Rohita Sinha, 2010 .

Computing the Dynamic Supramolecular Structural Proteome

Ruth Nussinov, Jason A. Papin, Ilya A. Vakser, 2017, PLoS Comput. Biol..

A simple shape characteristic of protein-protein recognition

Ilya A. Vakser, George Nicola, 2007, Bioinform..

A simple shape characteristic of protein-protein recognition

Ilya A. Vakser, George Nicola, I. Vakser, 2007, Bioinform..

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

Deepak Singla, Petras J. Kundrotas, Ilya A. Vakser, 2015, BMC Bioinformatics.

Protein-Protein Docking Methods

Garland R. Marshall, Ilya A. Vakser, I. Vakser, 2005 .

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

Petras J. Kundrotas, Ilya A. Vakser, Taras Dauzhenka, 2018, J. Comput. Chem..

GWIDD: Genome-wide protein docking database

Petras J. Kundrotas, Ilya A. Vakser, Zhengwei Zhu, 2009, Nucleic Acids Res..

The ruggedness of protein-protein energy landscape and the cutoff for 1/rn potentials

Ilya A. Vakser, Anatoly M. Ruvinsky, I. Vakser, 2008, Bioinform..

Protein Docking in the Absence of Detailed Molecular Structures

Ilya A. Vakser, I. Vakser, G. Nikiforovich, 1995 .

Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?

Petras J. Kundrotas, Ilya A. Vakser, Rohita Sinha, 2012, PloS one.