New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy. - Anatoly M. Ruvinsky; A. V. Kozintsev (J. Comput. Chem., 2005)

Calculations of protein-ligand binding entropy of relative and overall molecular motions. - Anatoly M. Ruvinsky (J. Comput. Aided Mol. Des., 2007)

Role of binding entropy in the refinement of protein-ligand docking predictions: Analysis based on the use of 11 scoring functions. - Anatoly M. Ruvinsky (J. Comput. Chem., 2007)

The ruggedness of protein-protein energy landscape and the cutoff for 1/rn potentials. - Anatoly M. Ruvinsky; Ilya A. Vakser (Bioinform., 2009)

Correlation analysis of the side-chains conformational distribution in bound and unbound proteins. - Tatsiana Kirys; Anatoly M. Ruvinsky; Alexander V. Tuzikov; Ilya A. Vakser (BMC Bioinform., 2012)

Structure fluctuations and conformational Changes in protein binding. - Anatoly M. Ruvinsky; Tatsiana Kirys; Alexander V. Tuzikov; Ilya A. Vakser (J. Bioinform. Comput. Biol., 2012)

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)

Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics. - S. Roy Kimura; Hai Peng Hu; Anatoly M. Ruvinsky; Woody Sherman; Angelo D. Favia (J. Chem. Inf. Model., 2017)