37 citations · 43 across the 7 of their papers we have counts for
7 papers
Ensemble-based characterization of unbound and bound states on protein energy landscape
Anatoly M. Ruvinsky, Tatsiana Kirys, Alexander V. Tuzikov +1
Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound a…
Structure fluctuations and conformational changes in protein binding
Anatoly M. Ruvinsky, Tatsiana Kirys, Alexander V. Tuzikov +1
Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the…
Side-chain conformational changes upon protein-protein association
Anatoly M. Ruvinsky, Tatsiana Kirys, Alexander V. Tuzikov +1
Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational ch…
Sequence composition and environment effects on residue fluctuations in protein structures
Anatoly M. Ruvinsky, Ilya A. Vakser
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transition…
The ruggedness of protein-protein energy landscape and the cutoff for 1/r^n potentials
Anatoly M. Ruvinsky, Ilya A. Vakser
The interaction cutoff contribution to the ruggedness of protein-protein energy landscape (the artificial ruggedness) is studied in terms of relative energy fluctuations for 1/r^n…
The role of binding entropy in the refinement of protein-ligand docking predictions: analysis based on the use of 11 scoring functions
Anatoly M. Ruvinsky
We present results of testing of the ability of eleven popular scoring functions to predict native docked positions using a recently developed method [1] for estimation the entropy…