DOI: 10.1073/pnas.0611593104. Near-native structure refinement using <i>in vacuo</i> energy minimization

Near-native structure refinement using in vacuo energy minimization

10.1073/pnas.0611593104

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

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.

Bibliography

Summa, C. M., & Levitt, M. (2007). Near-native structure refinement using in vacuo energy minimization. Proceedings of the National Academy of Sciences, 104(9), 3177â3182.

Authors 2

Christopher M. Summa (first)
Michael Levitt (additional)

References 41 Referenced 124

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Dates

Type	When
Created	18 years, 6 months ago (Feb. 21, 2007, 12:04 a.m.)
Deposited	3 years, 4 months ago (April 12, 2022, 3:50 p.m.)
Indexed	1 month ago (July 22, 2025, 6:56 a.m.)
Issued	18 years, 5 months ago (Feb. 27, 2007)
Published	18 years, 5 months ago (Feb. 27, 2007)
Published Online	18 years, 5 months ago (Feb. 27, 2007)
Published Print	18 years, 5 months ago (Feb. 27, 2007)

Funders 0

None

BibTeX

@article{Summa_2007, title={Near-native structure refinement using in vacuo energy minimization}, volume={104}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.0611593104}, DOI={10.1073/pnas.0611593104}, number={9}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Summa, Christopher M. and Levitt, Michael}, year={2007}, month=feb, pages={3177–3182} }

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