Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives. - Petras J. Kundrotas; Emil Alexov (BMC Bioinform., 2006)

Assessing the Quality of the Homology-Modeled 3D Structures from electrostatic Standpoint: Test on bacterial nucleoside monophosphate kinase Families. - Petras J. Kundrotas; Paulina Georgieva; Alexandra Shosheva; Petya Christova; Emil Alexov (J. Bioinform. Comput. Biol., 2007)

PROTCOM: searchable database of protein complexes enhanced with domain-domain structures. - Petras J. Kundrotas; Emil Alexov (Nucleic Acids Res., 2007)

GWIDD: Genome-wide protein docking database. - Petras J. Kundrotas; Zhengwei Zhu 001; Ilya A. Vakser (Nucleic Acids Res., 2010)

Accuracy of Protein-Protein Binding Sites in High-Throughput Template-Based Modeling. - Petras J. Kundrotas; Ilya A. Vakser (PLoS Comput. Biol., 2010)

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)

Text Mining for Protein Docking. - Varsha D. Badal; Petras J. Kundrotas; Ilya A. Vakser (PLoS Comput. Biol., 2015)

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 (ISBRA, 2016)

Template-Based Modeling of Protein-RNA Interactions. - Jinfang Zheng; Petras J. Kundrotas; Ilya A. Vakser; Shiyong Liu (PLoS Comput. Biol., 2016)

Natural language processing in text mining for structural modeling of protein complexes. - Varsha D. Badal; Petras J. Kundrotas; Ilya A. Vakser (BMC Bioinform., 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)

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)

Text mining for modeling of protein complexes enhanced by machine learning. - Varsha D. Badal; Petras J. Kundrotas; Ilya A. Vakser (Bioinform., 2021)