Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives.

ABSTRACT: Biomolecular recognition such as binding of small molecules, nucleic acids, peptides and proteins to their target receptors plays key roles in cellular function and has been targeted for therapeutic drug design. Molecular dynamics (MD) is a computational approach to analyze these binding processes at an atomistic level, which provides valuable understandings of the mechanisms of biomolecular recognition. However, the rather slow biomolecular binding events often present challenges for conventional MD (cMD), due to limited simulation timescales (typically over hundreds of nanoseconds to tens of microseconds). In this regard, enhanced sampling methods, particularly accelerated MD (aMD), have proven useful to bridge the gap and enable all-atom simulations of biomolecular binding events. Here,

SUBMITTER: Pawnikar S 

PROVIDER: S-EPMC8747661 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature