Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking.

ABSTRACT: Multicanonical molecular dynamics (McMD)-based dynamic docking is a powerful tool to not only predict the native binding configuration between two flexible molecules, but it can also be used to accurately simulate the binding/unbinding pathway. Furthermore, it can also predict alternative binding sites, including allosteric ones, by employing an exhaustive sampling approach. Since McMD-based dynamic docking accurately samples binding/unbinding events, it can thus be used to determine the molecular mechanism of binding between two molecules. We developed the McMD-based dynamic docking methodology based on the powerful, but woefully underutilized McMD algorithm, combined with a toolset to perform the docking and to analyze the results. Here, we showcase three of our recent works, where we ha

SUBMITTER: Bekker GJ 

PROVIDER: S-EPMC9842809 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature