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Three enhancements to the inference of statistical protein-DNA potentials.
MedLine Citation:
PMID:  23042633     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
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.
Authors:
Mohammed Alquraishi; Harley H McAdams
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-10-8
Journal Detail:
Title:  Proteins     Volume:  -     ISSN:  1097-0134     ISO Abbreviation:  Proteins     Publication Date:  2012 Oct 
Date Detail:
Created Date:  2012-10-8     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  8700181     Medline TA:  Proteins     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
Copyright © 2012 Wiley Periodicals, Inc.
Affiliation:
Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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