Reliable Generation of Native-Like Decoys Limits Predictive Ability in Fragment-Based Protein Structure Prediction.

ABSTRACT: Our previous work with fragment-assembly methods has demonstrated specific deficiencies in conformational sampling behaviour that, when addressed through improved sampling algorithms, can lead to more reliable prediction of tertiary protein structure when good fragments are available, and when score values can be relied upon to guide the search to the native basin. In this paper, we present preliminary investigations into two important questions arising from more difficult prediction problems. First, we investigated the extent to which native-like conformational states are generated during multiple runs of our search protocols. We determined that, in cases of difficult prediction, native-like decoys are rarely or never generated. Second, we developed a scheme for decoy retention that balan

SUBMITTER: Kandathil SM 

PROVIDER: S-EPMC6843117 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature