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

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.

Journal article Genome biology Genome Biol. 2008 Apr 8;9(4):R68.