Development of the force field parameters for phosphoimidazole and phosphohistidine. - Yuri A. Kosinsky; Pavel E. Volynsky; Philippe Lagant; Gérard Vergoten; Ei-Ichiro Suzuki; Alexander S. Arseniev; Roman G. Efremov (J. Comput. Chem., 2004)

Association of transmembrane helices: what determines assembling of a dimer? - Roman G. Efremov; Yana A. Vereshaga; Pavel E. Volynsky; Dmitry E. Nolde; Alexander S. Arseniev (J. Comput. Aided Mol. Des., 2006)

Computer Simulations of Membrane-Lytic peptides: Perspectives in Drug Design. - Anton A. Polyansky; Pavel E. Volynsky; Roman G. Efremov (J. Bioinform. Comput. Biol., 2007)

Method To Assess Packing Quality of Transmembrane α-Helices in Proteins, 1. Parametrization Using Structural Data. - Anton O. Chugunov; Valery N. Novoseletsky; Dmitry E. Nolde; Alexander S. Arseniev; Roman G. Efremov (J. Chem. Inf. Model., 2007)

Method To Assess Packing Quality of Transmembrane α-Helices in Proteins, 2. Validation by "Correct vs Misleading" Test. - Anton O. Chugunov; Valery N. Novoseletsky; Dmitry E. Nolde; Alexander S. Arseniev; Roman G. Efremov (J. Chem. Inf. Model., 2007)

Docking of ATP to Ca-ATPase: Considering Protein Domain Motions. - Timothy V. Pyrkov; Yuri A. Kosinsky; Alexander S. Arseniev; John P. Priestle; Edgar Jacoby; Roman G. Efremov (J. Chem. Inf. Model., 2007)

PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes. - Timothy V. Pyrkov; Anton O. Chugunov; Nikolay A. Krylov; Dmitry E. Nolde; Roman G. Efremov (Bioinform., 2009)

PREDDIMER: a web server for prediction of transmembrane helical dimers. - Anton A. Polyansky; Anton O. Chugunov; Pavel E. Volynsky; Nikolay A. Krylov; Dmitry E. Nolde; Roman G. Efremov (Bioinform., 2014)

Deciphering Fine Molecular Details of Proteins' Structure and Function with a Protein Surface Topography (PST) Method. - Anna D. Koromyslova; Anton O. Chugunov; Roman G. Efremov (J. Chem. Inf. Model., 2014)

Cardiotoxins: Functional Role of Local Conformational Changes. - Anastasia G. Konshina; Nikolay A. Krylov; Roman G. Efremov (J. Chem. Inf. Model., 2017)

Dielectric-Dependent Strength of Interlipid Hydrogen Bonding in Biomembranes: Model Case Study. - Roman G. Efremov (J. Chem. Inf. Model., 2019)

Stepwise Insertion of Cobra Cardiotoxin CT2 into a Lipid Bilayer Occurs as an Interplay of Protein and Membrane "Dynamic Molecular Portraits". - Anastasia G. Konshina; Peter V. Dubovskii; Roman G. Efremov (J. Chem. Inf. Model., 2021)

Structure-based prediction of T cell receptor recognition of unseen epitopes using TCRen. - Vadim K. Karnaukhov; Dmitrii S. Shcherbinin; Anton O. Chugunov; Dmitriy M. Chudakov; Roman G. Efremov; Ivan V. Zvyagin; Mikhail Shugay (Nat. Comput. Sci., 2024)