A conformation ensemble approach to protein residue-residue contact
1 Department of Computer Science, University of Missouri, Columbia, MO 65211, USA
2 Informatics Institute, University of Missouri, Columbia, MO 65211, USA
3 C. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA
BMC Structural Biology 2011, 11:38 doi:10.1186/1472-6807-11-38Published: 12 October 2011
Protein residue-residue contact prediction is important for protein model generation and model evaluation. Here we develop a conformation ensemble approach to improve residue-residue contact prediction. We collect a number of structural models stemming from a variety of methods and implementations. The various models capture slightly different conformations and contain complementary information which can be pooled together to capture recurrent, and therefore more likely, residue-residue contacts.
We applied our conformation ensemble approach to free modeling targets from both CASP8 and CASP9. Given a diverse ensemble of models, the method is able to achieve accuracies of. 48 for the top L/5 medium range contacts and. 36 for the top L/5 long range contacts for CASP8 targets (L being the target domain length). When applied to targets from CASP9, the accuracies of the top L/5 medium and long range contact predictions were. 34 and. 30 respectively.
When operating on a moderately diverse ensemble of models, the conformation ensemble approach is an effective means to identify medium and long range residue-residue contacts. An immediate benefit of the method is that when tied with a scoring scheme, it can be used to successfully rank models.