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

Alejandro Panjkovich1,3 email, Francisco Melo1 email and Marc A Marti-Renom2 email

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

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

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

author email corresponding author email

Genome Biology 2008, 9:R68doi:10.1186/gb-2008-9-4-r68

Published: 8 April 2008

Subject areas: Bioinformatics, Methods

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.


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