Folding proteins with a simple energy function and extensive conformational searching.
We describe a computer algorithm for predicting the three-dimensional structures of proteins using only their amino acid sequences. The method differs from others in two ways: (1) it uses very few energy parameters, representing hydrophobic and polar interactions, and (2) it uses a new "constraint-based exhaustive" searching method, which appears to be among the fastest and most complete search methods yet available for realistic protein models. It finds a relatively small number of low-energy conformations, among which are native-like conformations, for crambin (1CRN), avian pancreatic polypeptide (1PPT), melittin (2MLT), and apamin. Thus, the lowest-energy states of very simple energy functions may predict the native structures of globular proteins.
Yue
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Department of Pharmaceutical Chemistry, University of California at San Francisco, 94143, USA.
Dill
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D000465:Algorithms; D000595:Amino Acid Sequence; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D013816:Thermodynamics