Using scores derived from statistical coupling analysis to distinguish correct and incorrect folds in de‐novo protein structure prediction
- 14 November 2007
- journal article
- research article
- Published by Wiley in Proteins-Structure Function and Bioinformatics
- Vol. 71 (2), 950-959
- https://doi.org/10.1002/prot.21779
Abstract
Distinguishing native from non-native folds remains a challenging problem for protein structure prediction. We describe a method, SCA-distance scoring, based on results from statistical coupling analysis which discriminates between native and non-native folds produced by a de novo protein structure prediction method for four out of five test proteins. The method is particularly good at discriminating non-native folds which are close in RMSD to the true fold but contain a change in an internal structural element. SCA-distance scoring is a useful addition to the tools available for distinguishing native from non-native folds in protein structure prediction. Proteins 2008.Keywords
This publication has 33 references indexed in Scilit:
- Protein model refinement using structural fragment tessellationComputational Biology and Chemistry, 2006
- Pfam: clans, web tools and servicesNucleic Acids Research, 2006
- Predicting protein interaction sites from residue spatial sequence profile and evolution rateFEBS Letters, 2005
- An Evolutionarily Conserved Network of Amino Acids Mediates Gating in Voltage-dependent Potassium ChannelsJournal of Molecular Biology, 2004
- On Evolutionary Conservation of Thermodynamic Coupling in ProteinsJournal of Biological Chemistry, 2004
- Evolutionarily conserved networks of residues mediate allosteric communication in proteinsNature Structural & Molecular Biology, 2002
- Effective use of sequence correlation and conservation in fold recognitionJournal of Molecular Biology, 1999
- Coevolving protein residues: maximum likelihood identification and relationship to structureJournal of Molecular Biology, 1999
- The prediction of protein contacts from multiple sequence alignmentsProtein Engineering, Design and Selection, 1996
- Global Fold Determination from a Small Number of Distance RestraintsJournal of Molecular Biology, 1995