ClustENMD: Efficient sampling of biomolecular conformational space at atomic resolution

Abstract

SummaryEfficient sampling of conformational space is essential for elucidating functional/allosteric mechanisms of proteins and generating ensembles of conformers for docking applications. However, unbiased sampling is still a challenge especially for highly flexible and/or large systems. To address this challenge, we describe the new implementation of our computationally efficient algorithm ClustENMD that is integrated with ProDy and OpenMM softwares. This hybrid method performs iterative cycles of conformer generation using elastic network model (ENM) for deformations along global modes, followed by clustering and short molecular dynamics (MD) simulations. ProDy framework enables full automation and analysis of generated conformers and visualization of their distributions in the essential subspace. Availability and implementationClustENMD is open-source and freely available under MIT License from https://github.com/prody/ProDy. Contactburak.kaynak@pitt.edu or doruker@pitt.edu Supplementary informationSupplementary materials comprise method details, figures, table and tutorial.