3DRobot: automated generation of diverse and well-packed protein structure decoys.

ABSTRACT:

Motivation

Computationally generated non-native protein structure conformations (or decoys) are often used for designing protein folding simulation methods and force fields. However, almost all the decoy sets currently used in literature suffer from uneven root mean square deviation (RMSD) distribution with bias to non-protein like hydrogen-bonding and compactness patterns. Meanwhile, most protein decoy sets are pre-calculated and there is a lack of methods for automated generation of high-quality decoys for any target proteins.

Results

We developed a new algorithm, 3DRobot, to create protein structure decoys by free fragment assembly with enhanced hydrogen-bonding and compactness interactions. The method was benchmarked with three widely used decoy sets from ab initio foldi

SUBMITTER: Deng H 

PROVIDER: S-EPMC5006309 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature