FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling.

ABSTRACT:

Motivation

Speed, accuracy and robustness of building protein fragment library have important implications in de novo protein structure prediction since fragment-based methods are one of the most successful approaches in template-free modeling (FM). Majority of the existing fragment detection methods rely on database-driven search strategies to identify candidate fragments, which are inherently time-consuming and often hinder the possibility to locate longer fragments due to the limited sizes of databases. Also, it is difficult to alleviate the effect of noisy sequence-based predicted features such as secondary structures on the quality of fragment.

Results

Here, we present FRAGSION, a database-free method to efficiently generate protein fragment library by sampling from an

SUBMITTER: Bhattacharya D 

PROVIDER: S-EPMC4920111 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature