Localization of binding sites in protein structures by optimization of a composite scoring function.

Localization of binding sites in protein structures by optimization of a composite scoring function. Research Abstract Details 

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Localization of binding sites in protein structures by optimization of a composite scoring function. Abstract Text:

Andrea Rossi,Marc A Marti-Renom,Andrej Sali,

The rise in the number of functionally uncharacterized protein structures is increasing the demand for structure-based methods for functional annotation. Here, we describe a method for predicting the location of a binding site of a given type on a target protein structure. The method begins by constructing a scoring function, followed by a Monte Carlo optimization, to find a good scoring patch on the protein surface. The scoring function is a weighted linear combination of the z-scores of various properties of protein structure and sequence, including amino acid residue conservation, compactness, protrusion, convexity, rigidity, hydrophobicity, and charge density; the weights are calculated from a set of previously identified instances of the binding-site type on known protein structures. The scoring function can easily incorporate different types of information useful in localization, thus increasing the applicability and accuracy of the approach. To test the method, 1008 known protein structures were split into 20 different groups according to the type of the bound ligand. For nonsugar ligands, such as various nucleotides, binding sites were correctly identified in 55%-73% of the cases. The method is completely automated (http://salilab.org/patcher) and can be applied on a large scale in a structural genomics setting.

Localization of binding sites in protein structures by optimization of a composite scoring function. Publishing Authors By Initials

A Rossi,MA Marti-Renom,A Sali,

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Localization of binding sites in protein structures by optimization of a composite scoring function. Journal Published:

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: Protein science : a publication of the Protein Soc

VOLUME: 15

Page Numbers: 2366-80

Journal Abbreviation: Protein Sci.

ISSN: 0961-8368

DAY: 8

MONTH: 09

YEAR: 2006

Localization of binding sites in protein structures by optimization of a composite scoring function. Information

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LANGUAGE: eng

NlmUniqueID: 9211750

Localization of binding sites in protein structures by optimization of a composite scoring function. Keywords Mesh Terms:

KEYWORDS: Proteins

MESH TERMS: chemistry

Chemical & Substance for Abstract: Localization of binding sites in protein structures by optimization of a composite scoring function. Information

Substance Name: Proteins

Registry Number: 0

Grant and Affiliation Information for Localization of binding sites in protein structures by optimization of a composite scoring function.

AFFILIATION: Department of Biopharmaceutical Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Research, University of California, San Francisco, California 94143-2552, USA. andrea@salilab.org

Country: United States

AGENCY: United States NIGMS

GRANT: R01 GM54762

ACRONYM: GM

MEDLINETA: Protein Sci

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