Gennady M. Verkhivker

TL;DR: This work sets out to develop a strategy for flexible docking by combining a simple model of ligand-protein interactions for molecular recognition with an evolutionary programming search technique, and develops an intermolecular energy function that incorporates steric and hydrogen-bonding terms.

TL;DR: This protocol resolves some common failures in ligand-protein docking and detects crystallographic binding modes that were not found during docking simulations and proposes a proposed hierarchical approach that involves a hierarchy of energy functions.

TL;DR: A package of computer programs for molecular dynamics simulations-MOIL-is described, which enables the study of macromolecules with potentials consistent with the AMBER/OPLS force field.

TL;DR: A comprehensive computational analysis of the Hsp90 communication pathways and dynamics at atomic resolution has revealed the role of the nucleotide in effecting conformational changes, elucidating the mechanisms of signal propagation and determining “hot spots” involved in interdomain communication pathways from theucleotide-binding site to the C-terminal domain interface.

TL;DR: The proposed approach provides reasonable estimates of distinctions in binding affinity and gives an insight into the nature of enthalpyentropy compensation factors detected in the binding process.