Folding proteins with a simple energy function and extensive conformational searching.

K Yue; K A Dill

doi:10.1002/pro.5560050209

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Folding proteins with a simple energy function and extensive conformational searching.

K Yue·K A Dill

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Abstract

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.

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Algorithms Amino Acid Sequence Chemical Phenomena Chemistry, Physical Computer Simulation Models, Molecular Molecular Sequence Data Protein Conformation Protein Folding Thermodynamics Journal Article Research Support, U.S. Gov't, Non-P.H.S.

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K Yue, K A Dill. 1996. Folding proteins with a simple energy function and extensive conformational searching.. https://doi.org/10.1002/pro.5560050209

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