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

Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile. fmelo@bio.puc.cl.

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 - as supplied by publisher]

PMCID: PMC2643939