Thermal Titration Molecular Dynamics (TTMD): Not Your Usual Post-Docking Refinement.

ABSTRACT: Molecular docking is one of the most widely used computational approaches in the field of rational drug design, thanks to its favorable balance between the rapidity of execution and the accuracy of provided results. Although very efficient in exploring the conformational degrees of freedom available to the ligand, docking programs can sometimes suffer from inaccurate scoring and ranking of generated poses. To address this issue, several post-docking filters and refinement protocols have been proposed throughout the years, including pharmacophore models and molecular dynamics simulations. In this work, we present the first application of Thermal Titration Molecular Dynamics (TTMD), a recently developed method for the qualitative estimation of protein-ligand unbinding kinetics, to the refine

SUBMITTER: Menin S 

PROVIDER: S-EPMC9968212 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature