RIP-MD: a tool to study residue interaction networks in protein molecular dynamics.

ABSTRACT: Protein structure is not static; residues undergo conformational rearrangements and, in doing so, create, stabilize or break non-covalent interactions. Molecular dynamics (MD) is a technique used to simulate these movements with atomic resolution. However, given the data-intensive nature of the technique, gathering relevant information from MD simulations is a complex and time consuming process requiring several computational tools to perform these analyses. Among different approaches, the study of residue interaction networks (RINs) has proven to facilitate the study of protein structures. In a RIN, nodes represent amino-acid residues and the connections between them depict non-covalent interactions. Here, we describe residue interaction networks in protein molecular dynamics (RIP-MD), a

SUBMITTER: Contreras-Riquelme S 

PROVIDER: S-EPMC6287582 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature