Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction.

ABSTRACT:

Motivation

Decoy datasets, consisting of a solved protein structure and numerous alternative native-like structures, are in common use for the evaluation of scoring functions in protein structure prediction. Several pitfalls with the use of these datasets have been identified in the literature, as well as useful guidelines for generating more effective decoy datasets. We contribute to this ongoing discussion an empirical assessment of several decoy datasets commonly used in experimental studies.

Results

We find that artefacts and sampling issues in the large majority of these data make it trivial to discriminate the native structure. This underlines that evaluation based on the rank/z-score of the native is a weak test of scoring function performance. Moreover, sampling bias

SUBMITTER: Handl J 

PROVIDER: S-EPMC2677743 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature