Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 104, Issue 9, Pages 3177-3182Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0611593104
Keywords
protein; empirical potential; molecular mechanics potential; knowledge-based; protein structure refinement
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Funding
- NIGMS NIH HHS [R01 GM063817-08, R01 GM063817, GM63817] Funding Source: Medline
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One of the greatest shortcomings of macromolecular energy minimization and molecular dynamics techniques is that they generally do not preserve the native structure of proteins as observed by x-ray crystallography. This deformation of the native structure means that these methods are not generally used to refine structures produced by homology-modeling techniques. Here, we use a database of 75 proteins to test the ability of a variety of popular molecular mechanics force fields to maintain the native structure. Minimization from the native structure is a weak test of potential energy functions: It is complemented by a much stronger test in which the same methods are compared for their ability to attract a near-native decoy protein structure toward the native structure. We use a powerfully convergent energy-minimization method and show that, of the traditional molecular mechanics potentials tested, only one showed a modest net improvement over a large data set of structurally diverse proteins. A smooth, differentiable knowledge-based pairwise atomic potential performs better on this test than traditional potential functions. This work is expected to have important implications for protein structure refinement, homology modeling, and structure prediction.
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