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Genome Biol. 2008 Apr 8;9(4):R68. doi: 10.1186/gb-2008-9-4-r68.

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

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

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.

PMID:
18397517
[PubMed - indexed for MEDLINE]
PMCID:
PMC2643939
Free PMC Article

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