An improved protein decoy set for testing energy functions for protein structure prediction

TitleAn improved protein decoy set for testing energy functions for protein structure prediction
Publication TypeJournal Article
Year of Publication2003
AuthorsTsai, J., Bonneau R., Morozov A. V., Kuhlman B., Rohl C. A., & Baker D.
JournalProteins
Volume53
Issue1
Pagination76-87
Date Published2003 Oct 1
ISSN1097-0134
KeywordsAlgorithms, Hydrogen Bonding, Primary Publication, Protein Conformation, Proteins, Solvents
Abstract

We have improved the original Rosetta centroid/backbone decoy set by increasing the number of proteins and frequency of near native models and by building on sidechains and minimizing clashes. The new set consists of 1,400 model structures for 78 different and diverse protein targets and provides a challenging set for the testing and evaluation of scoring functions. We evaluated the extent to which a variety of all-atom energy functions could identify the native and close-to-native structures in the new decoy sets. Of various implicit solvent models, we found that a solvent-accessible surface area-based solvation provided the best enrichment and discrimination of close-to-native decoys. The combination of this solvation treatment with Lennard Jones terms and the original Rosetta energy provided better enrichment and discrimination than any of the individual terms. The results also highlight the differences in accuracy of NMR and X-ray crystal structures: a large energy gap was observed between native and non-native conformations for X-ray structures but not for NMR structures.

Alternate JournalProteins
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