Document Detail

Three enhancements to the inference of statistical protein-DNA potentials.
MedLine Citation:
PMID:  23042633     Owner:  NLM     Status:  MEDLINE    
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 inference that 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-DNA modeling, and we show that they can improve the accuracy of predicted DNA binding sites by up to 21%.
Mohammed AlQuraishi; Harley H McAdams
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2012-11-12
Journal Detail:
Title:  Proteins     Volume:  81     ISSN:  1097-0134     ISO Abbreviation:  Proteins     Publication Date:  2013 Mar 
Date Detail:
Created Date:  2013-01-28     Completed Date:  2013-08-02     Revised Date:  2014-08-06    
Medline Journal Info:
Nlm Unique ID:  8700181     Medline TA:  Proteins     Country:  United States    
Other Details:
Languages:  eng     Pagination:  426-42     Citation Subset:  IM    
Copyright Information:
Copyright © 2012 Wiley Periodicals, Inc.
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MeSH Terms
Artificial Intelligence
Base Sequence
Binding Sites
Consensus Sequence
Crystallography, X-Ray
DNA / chemistry*
DNA-Binding Proteins / chemistry
Data Interpretation, Statistical
Models, Molecular
Models, Statistical
Protein Binding
Protein Interaction Mapping / methods*
Proteins / chemistry*
Sensitivity and Specificity
Grant Support
Reg. No./Substance:
0/DNA-Binding Proteins; 0/Proteins; 9007-49-2/DNA

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