Near-native structure refinement using in vacuo energy minimization.

Near-native structure refinement using in vacuo energy minimization. Research Abstract Details 

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Near-native structure refinement using in vacuo energy minimization. Abstract Text:

Christopher M Summa,Michael Levitt,

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.

Near-native structure refinement using in vacuo energy minimization. Publishing Authors By Initials

CM Summa,M Levitt,

For similar proteins research abstracts see: proteins research

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Near-native structure refinement using in vacuo energy minimization. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Proceedings of the National Academy of Sciences of

VOLUME: 104

Page Numbers: 3177-82

Journal Abbreviation: Proc. Natl. Acad. Sci. U.S.A.

ISSN: 0027-8424

DAY: 20

MONTH: 02

YEAR: 2007

Near-native structure refinement using in vacuo energy minimization. Information

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LANGUAGE: eng

NlmUniqueID: 7505876

Near-native structure refinement using in vacuo energy minimization. Keywords Mesh Terms:

KEYWORDS: Proteins

MESH TERMS: chemistry

Chemical & Substance for Abstract: Near-native structure refinement using in vacuo energy minimization. Information

Substance Name: Proteins

Registry Number: 0

Grant and Affiliation Information for Near-native structure refinement using in vacuo energy minimization.

AFFILIATION: Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.

Country: United States

AGENCY: United States NIGMS

GRANT: GM63817

ACRONYM: GM

MEDLINETA: Proc Natl Acad Sci U S A

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