A protein folding potential that places the native states of a large number of proteins near a local minimum Public Deposited

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Creator
  • Crippen, Gordon M.
    • Other Affiliation: College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-1065, U.S.A
  • Chhajer, Mukesh
    • Affiliation: College of Arts and Sciences, Department of Chemistry
Abstract
  • 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 ~4 Å rmsd and 71 native conformations within ~6 Å 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.
Date of publication
Identifier
  • 12165098
  • doi:10.1186/1472-6807-2-4
Resource type
  • Article
Rights statement
  • In Copyright
Rights holder
  • Mukesh Chhajer et al.; licensee BioMed Central Ltd.
Journal title
  • BMC Structural Biology
Journal volume
  • 2
Journal issue
  • 1
Page start
  • 4
Language
  • English
Is the article or chapter peer-reviewed?
  • Yes
ISSN
  • 1472-6807
Bibliographic citation
  • BMC Structural Biology. 2002 Aug 06;2(1):4
Access
  • Open Access
Publisher
  • BioMed Central Ltd
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