pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families. - Dmitry A. Suplatov; Eugeny M. Kirilin; Mikhail Arbatsky; Vakil Takhaveev; Vytas K. Svedas (Nucleic Acids Res., 2014)

Parallel workflow manager for non-parallel bioinformatic applications to solve large-scale biological problems on a supercomputer. - Dmitry A. Suplatov; Nina Popova 001; Sergey A. Zhumatiy; Vladimir V. Voevodin; Vytas K. Svedas (J. Bioinform. Comput. Biol., 2016)

Mustguseal: a server for multiple structure-guided sequence alignment of protein families. - Dmitry A. Suplatov; Kirill E. Kopylov; Nina N. Popova; Vladimir V. Voevodin; Vytas K. Svedas (Bioinform., 2018)

The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families. - Dmitry A. Suplatov; Yana A. Sharapova; Daria Timonina; Kirill E. Kopylov; Vytas K. Svedas (J. Bioinform. Comput. Biol., 2018)

Simulating the Long-timescale Structural Behavior of Bacterial and Influenza Neuraminidases with Different HPC Resources. - Yana A. Sharapova; Dmitry A. Suplatov; Vytas K. Svedas (Supercomput. Front. Innov., 2018)

High-Performance Hybrid Computing for Bioinformatic Analysis of Protein Superfamilies. - Dmitry A. Suplatov; Yana A. Sharapova; Maksim V. Shegay; Nina N. Popova; Kateryna Fesko; Vladimir V. Voevodin; Vytas K. Svedas (RuSCDays, 2019)

parMATT: parallel multiple alignment of protein 3D-structures with translations and twists for distributed-memory systems. - Maksim V. Shegay; Dmitry A. Suplatov; Nina N. Popova; Vytas K. Svedas; Vladimir V. Voevodin (Bioinform., 2019)

Yosshi: a web-server for disulfide engineering by bioinformatic analysis of diverse protein families. - Dmitry A. Suplatov; Daria Timonina; Yana A. Sharapova; Vytas K. Svedas (Nucleic Acids Res., 2019)

EasyAmber: A comprehensive toolbox to automate the molecular dynamics simulation of proteins. - Dmitry A. Suplatov; Yana A. Sharapova; Vytas K. Svedas (J. Bioinform. Comput. Biol., 2020)

vsFilt: A Tool to Improve Virtual Screening by Structural Filtration of Docking Poses. - Irina V. Gushchina; Aleksandra M. Polenova; Dmitry A. Suplatov; Vytas K. Svedas; Dmitry K. Nilov (J. Chem. Inf. Model., 2020)

Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies. - Dmitry A. Suplatov; Yana A. Sharapova; Elizaveta Geraseva; Vytas K. Svedas (Nucleic Acids Res., 2020)

PLUMED Plugin Integration into High Performance Pmemd Program for Enhanced Molecular Dynamics Simulations. - Viktor V. Drobot; Evgeny M. Kirilin; Kirill E. Kopylov; Vytas K. Svedas (Supercomput. Front. Innov., 2021)

Co-designing HPC-systems by computing capabilities and management flexibility to accommodate bioinformatic workflows at different complexity levels. - Dmitry A. Suplatov; Maksim V. Shegay; Yana A. Sharapova; Ivan V. Timokhin; Nina Popova 001; Vladimir V. Voevodin; Vytas K. Svedas (J. Supercomput., 2021)

Guide tree optimization with genetic algorithm to improve multiple protein 3D-structure alignment. - Maksim V. Shegay; Vytas K. Svedas; Vladimir V. Voevodin; Dmitry A. Suplatov; Nina N. Popova (Bioinform., 2022)