SMOG 2: A Versatile Software Package for Generating Structure-Based Models.

ABSTRACT: Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural i

SUBMITTER: Noel JK 

PROVIDER: S-EPMC4786265 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature