Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods.

ABSTRACT: The ability to efficiently sample structurally diverse protein conformations allows one to gain a high-level view of a protein's energy landscape. Algorithms from robot motion planning have been used for conformational sampling, and several of these algorithms promote diversity by keeping track of "coverage" in conformational space based on the local sampling density. However, large proteins present special challenges. In particular, larger systems require running many concurrent instances of these algorithms, but these algorithms can quickly become memory intensive because they typically keep previously sampled conformations in memory to maintain coverage estimates. In addition, robotics-inspired algorithms depend on defining useful perturbation strategies for exploring the conformational

SUBMITTER: Abella JR 

PROVIDER: S-EPMC5756939 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature