Loop modeling: Sampling, filtering, and scoring.

Loop modeling: Sampling, filtering, and scoring. Research Abstract Details 

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Loop modeling: Sampling, filtering, and scoring. Abstract Text:

Cinque S Soto,Marc Fasnacht,Jiang Zhu,Lucy Forrest,Barry Honig,

We describe a fast and accurate protocol, LoopBuilder, for the prediction of loop conformations in proteins. The procedure includes extensive sampling of backbone conformations, side chain addition, the use of a statistical potential to select a subset of these conformations, and, finally, an energy minimization and ranking with an all-atom force field. We find that the Direct Tweak algorithm used in the previously developed LOOPY program is successful in generating an ensemble of conformations that on average are closer to the native conformation than those generated by other methods. An important feature of Direct Tweak is that it checks for interactions between the loop and the rest of the protein during the loop closure process. DFIRE is found to be a particularly effective statistical potential that can bias conformation space toward conformations that are close to the native structure. Its application as a filter prior to a full molecular mechanics energy minimization both improves prediction accuracy and offers a significant savings in computer time. Final scoring is based on the OPLS/SBG-NP force field implemented in the PLOP program. The approach is also shown to be quite successful in predicting loop conformations for cases where the native side chain conformations are assumed to be unknown, suggesting that it will prove effective in real homology modeling applications.

Loop modeling: Sampling, filtering, and scoring. Publishing Authors By Initials

CS Soto,M Fasnacht,J Zhu,L Forrest,B Honig,

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Loop modeling: Sampling, filtering, and scoring. Journal Published:

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

Journal: Proteins

VOLUME: 70

Page Numbers: 834-43

Journal Abbreviation: Proteins

ISSN: 1097-0134

DAY: 15

MONTH: Feb

YEAR: 2008

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LANGUAGE: eng

NlmUniqueID: 8700181

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Grant and Affiliation Information for Loop modeling: Sampling, filtering, and scoring.

AFFILIATION: Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.

Country: United States

AGENCY: United States NIGMS

GRANT: GM30518

ACRONYM: GM

MEDLINETA: Proteins

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