Chhajer M, Crippen GM. A protein folding potential that places the native states of a large number of proteins near a local minimum.
BMC STRUCTURAL BIOLOGY 2002;
2:4. [PMID:
12165098 PMCID:
PMC126205 DOI:
10.1186/1472-6807-2-4]
[Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2002] [Accepted: 08/06/2002] [Indexed: 11/22/2022]
Abstract
BACKGROUND
We present a simple method to train a potential function for the protein folding problem which, even though trained using a small number of proteins, is able to place a significantly large number of native conformations near a local minimum. The training relies on generating decoys by energy minimization of the native conformations using the current potential and using a physically meaningful objective function (derivative of energy with respect to torsion angles at the native conformation) during the quadratic programming to place the native conformation near a local minimum.
RESULTS
We also compare the performance of three different types of energy functions and find that while the pairwise energy function is trainable, a solvation energy function by itself is untrainable if decoys are generated by minimizing the current potential starting at the native conformation. The best results are obtained when a pairwise interaction energy function is used with solvation energy function.
CONCLUSIONS
We are able to train a potential function using six proteins which places a total of 42 native conformations within approximately 4 A rmsd and 71 native conformations within approximately 6 A rmsd of a local minimum out of a total of 91 proteins. Furthermore, the threading test using the same 91 proteins ranks 89 native conformations to be first and the other two as second.
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