Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.

ABSTRACT:

Motivation

Most current de novo structure prediction methods randomly sample protein conformations and thus require large amounts of computational resource. Here, we consider a sequential sampling strategy, building on ideas from recent experimental work which shows that many proteins fold cotranslationally.

Results

We have investigated whether a pseudo-greedy search approach, which begins sequentially from one of the termini, can improve the performance and accuracy of de novo protein structure prediction. We observed that our sequential approach converges when fewer than 20 000 decoys have been produced, fewer than commonly expected. Using our software, SAINT2, we also compared the run time and quality of models produced in a sequential fashion against a standard, non-sequ

SUBMITTER: de Oliveira SHP 

PROVIDER: S-EPMC6030820 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature