Building a better fragment library for de novo protein structure prediction.

ABSTRACT: Fragment-based approaches are the current standard for de novo protein structure prediction. These approaches rely on accurate and reliable fragment libraries to generate good structural models. In this work, we describe a novel method for structure fragment library generation and its application in fragment-based de novo protein structure prediction. The importance of correct testing procedures in assessing the quality of fragment libraries is demonstrated. In particular, the exclusion of homologs to the target from the libraries to correctly simulate a de novo protein structure prediction scenario, something which surprisingly is not always done. We demonstrate that fragments presenting different predominant predicted secondary structures should be treated differently during the fragment

SUBMITTER: de Oliveira SH 

PROVIDER: S-EPMC4406757 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature