Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds. - Mary Hongying Cheng; Robert D. Coalson; Michael Cascio; Maria G. Kurnikova (J. Comput. Aided Mol. Des., 2008)

Flexibility and Mobility in Mesophilic and Thermophilic homologous proteins from Molecular Dynamics and Foldunfold Method. - Tatyana B. Mamonova; Anna V. Glyakina; Maria G. Kurnikova; Oxana V. Galzitskaya (J. Bioinform. Comput. Biol., 2010)

An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations. - Arvind Ramanathan; Pratul K. Agarwal; Maria G. Kurnikova; Christopher James Langmead (J. Comput. Biol., 2010)

Exploring Protein Stability by Comparative Molecular Dynamics Simulations of Homologous Hyperthermophilic, Mesophilic, and Psychrophilic Proteins. - Sara Khan; Umar Farooq 005; Maria G. Kurnikova (J. Chem. Inf. Model., 2016)

Active Learning Guided Drug Design Lead Optimization Based on Relative Binding Free Energy Modeling. - Filipp Gusev; Evgeny Gutkin; Maria G. Kurnikova; Olexandr Isayev (J. Chem. Inf. Model., 2023)

CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. - Fengling Li; Suzanne Ackloo; Cheryl H. Arrowsmith; Fuqiang Ban; Christopher J. Barden; Hartmut Beck; Jan Beránek; Francois Berenger; Albina Bolotokova; Guillaume Bret; Marko Breznik; Emanuele Carosati; et al. (J. Chem. Inf. Model., 2024)

Active Learning-Guided Hit Optimization for the Leucine-Rich Repeat Kinase 2 WDR Domain Based on In Silico Ligand-Binding Affinities. - Filipp Gusev; Evgeny Gutkin; Francesco Gentile; Fuqiang Ban; S. Benjamin Koby; Fengling Li; Irene Chau; Suzanne Ackloo; Cheryl H. Arrowsmith; Albina Bolotokova; Pegah Ghiabi; Elisa Gibson; et al. (J. Chem. Inf. Model., 2025)

Automated On-the-Fly Optimization of Resource Allocation for Efficient Free Energy Simulations. - S. Benjamin Koby; Evgeny Gutkin; Shree Patel; Maria G. Kurnikova (J. Chem. Inf. Model., 2025)