Improving computational efficiency and tractability of protein design using a piecemeal approach. A strategy for parallel and distributed protein design.

ABSTRACT:

Motivation

Accuracy in protein design requires a fine-grained rotamer search, multiple backbone conformations, and a detailed energy function, creating a burden in runtime and memory requirements. A design task may be split into manageable pieces in both three-dimensional space and in the rotamer search space to produce small, fast jobs that are easily distributed. However, these jobs must overlap, presenting a problem in resolving conflicting solutions in the overlap regions.

Results

Piecemeal design, in which the design space is split into overlapping regions and rotamer search spaces, accelerates the design process whether jobs are run in series or in parallel. Large jobs that cannot fit in memory were made possible by splitting. Accepting the consensus amino acid selecti

SUBMITTER: Pitman DJ 

PROVIDER: S-EPMC3982153 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature