| Three enhancements to the inference of statistical protein-DNA potentials. | |
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MedLine Citation:
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PMID: 23042633 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
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The energetics of protein-DNA interactions are often modeled using so-called statistical potentials, that is, energy models derived from the atomic structures of protein-DNA complexes.Many statistical protein-DNA potentials based on differing theoretical assumptions have been investigated, but little attention has been paid to the types of data and the parameter estimation process used in deriving the statistical potentials.We describe three enhancements to statistical potential inferencethat significantly improve the accuracy of predicted protein-DNA interactions: (i) incorporation of binding energy data of protein-DNA complexes, in conjunction with their X-ray crystal structures, (ii) use of spatially-aware parameter fitting, and (iii) use of ensemble-based parameter fitting.We apply these enhancements to three widely-used statistical potentials and use the resulting enhanced potentials in a structure-based prediction of the DNA binding sites of proteins.These enhancements are directly applicable to all statistical potentials used in protein-DNAmodeling, and we show that they can improve the accuracy of predicted DNA binding sites by up to 21%. Proteins 2012. © 2012 Wiley Periodicals, Inc. |
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Authors:
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Mohammed Alquraishi; Harley H McAdams |
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Publication Detail:
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Type: JOURNAL ARTICLE Date: 2012-10-8 |
Journal Detail:
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Title: Proteins Volume: - ISSN: 1097-0134 ISO Abbreviation: Proteins Publication Date: 2012 Oct |
Date Detail:
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Created Date: 2012-10-8 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 8700181 Medline TA: Proteins Country: - |
Other Details:
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Languages: ENG Pagination: - Citation Subset: - |
Copyright Information:
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Copyright © 2012 Wiley Periodicals, Inc. |
Affiliation:
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Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA. |
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