Assessment of protein folding potentials with an evolutionary method.
Many different protein folding potentials have been developed in the last decades, based upon knowledge of experimentally determined protein structures. Decoy-based techniques are frequently used to assess these force fields, but other methods can explore different features in the performance of the interaction schemes, thus helping in their evaluation. Here, we propose an evolutionary strategy to efficiently assess folding potentials. We apply it to three potentials with different characteristics, taken from the bibliography. A search for minimum energy protein topologies, treated as arrangements of rigid protein fragments, is performed. The method, applied to a set of helix bundle proteins, shows the different behavior of the studied potentials, providing a reasonably fast tool to evaluate their advantages and limitations.
de Sancho
David
D
Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense, E-28040 Madrid, Spain.
Rey
Antonio
A
D000465:Algorithms; D000595:Amino Acid Sequence; D005075:Biological Evolution; D003198:Computer Simulation; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D020539:Sequence Analysis, Protein / Q000379:methods*
D011506:Proteins