Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods.

ABSTRACT: Recent years have seen several hybrid simulation methods for exploring the conformational space of proteins and their complexes or assemblies. These methods often combine fast analytical approaches with computationally expensive full atomic molecular dynamics (MD) simulations with the goal of rapidly sampling large and cooperative conformational changes at full atomic resolution. We present here a systematic comparison of the utility and limits of four such hybrid methods that have been introduced in recent years: MD with excited normal modes (MDeNM), collective modes-driven MD (CoMD), and elastic network model (ENM)-based generation, clustering, and relaxation of conformations (ClustENM) as well as its updated version integrated with MD simulations (ClustENMD). We analyzed the predicted c

SUBMITTER: Kaynak BT 

PROVIDER: S-EPMC8855042 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature