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Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs

Alejandro Panjkovich13, Francisco Melo1* and Marc A Marti-Renom2*

Author Affiliations

1 Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile

2 Structural Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF), Av. Autopista del Saler, 16, 46013 Valencia, Spain

3 Current address: Institute for Research in Biomedicine (IRB) and Barcelona Supercomputing Center (BSC), c/Josep Samitier 1-5, 08028 Barcelona, Spain

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Genome Biology 2008, 9:R68  doi:10.1186/gb-2008-9-4-r68

Published: 8 April 2008

Abstract

We introduce a new type of knowledge-based potentials for protein structure prediction, called 'evolutionary potentials', which are derived using a single experimental protein structure and all three-dimensional models of its homologous sequences. The new potentials have been benchmarked against other knowledge-based potentials, resulting in a significant increase in accuracy for model assessment. In contrast to standard knowledge-based potentials, we propose that evolutionary potentials capture key determinants of thermodynamic stability and specific sequence constraints required for fast folding.