| Robust recognition of zinc binding sites in proteins. | |
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MedLine Citation:
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PMID: 18042678 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Metals play a variety of roles in biological processes, and hence their presence in a protein structure can yield vital functional information. Because the residues that coordinate a metal often undergo conformational changes upon binding, detection of binding sites based on simple geometric criteria in proteins without bound metal is difficult. However, aspects of the physicochemical environment around a metal binding site are often conserved even when this structural rearrangement occurs. We have developed a Bayesian classifier using known zinc binding sites as positive training examples and nonmetal binding regions that nonetheless contain residues frequently observed in zinc sites as negative training examples. In order to allow variation in the exact positions of atoms, we average a variety of biochemical and biophysical properties in six concentric spherical shells around the site of interest. At a specificity of 99.8%, this method achieves 75.5% sensitivity in unbound proteins at a positive predictive value of 73.6%. We also test its accuracy on predicted protein structures obtained by homology modeling using templates with 30%-50% sequence identity to the target sequences. At a specificity of 99.8%, we correctly identify at least one zinc binding site in 65.5% of modeled proteins. Thus, in many cases, our model is accurate enough to identify metal binding sites in proteins of unknown structure for which no high sequence identity homologs of known structure exist. Both the source code and a Web interface are available to the public at http://feature.stanford.edu/metals. |
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Authors:
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Jessica C Ebert; Russ B Altman |
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Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural Date: 2007-11-27 |
Journal Detail:
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Title: Protein science : a publication of the Protein Society Volume: 17 ISSN: 0961-8368 ISO Abbreviation: Protein Sci. Publication Date: 2008 Jan |
Date Detail:
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Created Date: 2007-12-24 Completed Date: 2008-03-06 Revised Date: 2009-11-18 |
Medline Journal Info:
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Nlm Unique ID: 9211750 Medline TA: Protein Sci Country: United States |
Other Details:
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Languages: eng Pagination: 54-65 Citation Subset: IM |
Affiliation:
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Department of Genetics, Stanford University, Stanford, California 94305, USA. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Binding Sites Carrier Proteins / chemistry*, genetics, metabolism* Genomics Models, Biological Models, Molecular Protein Conformation Sensitivity and Specificity Zinc / chemistry*, metabolism* |
| Grant Support | |
ID/Acronym/Agency:
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LM05652/LM/NLM NIH HHS |
| Chemical | |
Reg. No./Substance:
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0/Carrier Proteins; 7440-66-6/Zinc |
| Comments/Corrections | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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