Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins.

ABSTRACT: Given by χ torsional angles, rotamers describe the side-chain conformations of amino acid residues in a protein based on the rotational isomers (hence the word rotamer). Constructed rotamer libraries, based on either protein crystal structures or dynamics studies, are the tools for classifying rotamers (torsional angles) in a way that reflect their frequency in nature. Rotamer libraries are routinely used in structure modeling and evaluation. In this perspective article, we would like to encourage researchers to apply rotamer analyses beyond their traditional use. Molecular dynamics (MD) of proteins highlight the in silico behavior of molecules in solution and thus can identify favorable side-chain conformations. In this article, we used simple computational tools to study rotamer dynamics

SUBMITTER: Haddad Y 

PROVIDER: S-EPMC6554459 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature