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Title: Protein–DNA Interactions: The Story so Far and a New Method for Prediction

Abstract

This review describes methods for the prediction of DNA binding function, and specifically summarizes a new method using 3D structural templates. The new method features the HTH motif that is found in approximately one-third of DNAbinding protein families. A library of 3D structural templates of HTH motifs was derived from proteins in the PDB. Templates were scanned against complete protein structures and the optimal superposition of a template on a structure calculated. Significance thresholds in terms of a minimum root mean squared deviation (rmsd) of an optimal superposition, and a minimum motif accessible surface area (ASA), have been calculated. In this way, it is possible to scan the template library against proteins of unknown function to make predictions about DNA-binding functionality.

Authors:
 [1];  [1]
  1. EMBL –European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1198266
Grant/Contract Number:  
FG02-96ER62166
Resource Type:
Published Article
Journal Name:
Comparative and Functional Genomics
Additional Journal Information:
Journal Name: Comparative and Functional Genomics Journal Volume: 4 Journal Issue: 4; Journal ID: ISSN 1531-6912
Publisher:
Hindawi Publishing Corporation
Country of Publication:
Country unknown/Code not available
Language:
English

Citation Formats

Jones, Susan, and Thornton, Janet M. Protein–DNA Interactions: The Story so Far and a New Method for Prediction. Country unknown/Code not available: N. p., 2003. Web. doi:10.1002/cfg.303.
Jones, Susan, & Thornton, Janet M. Protein–DNA Interactions: The Story so Far and a New Method for Prediction. Country unknown/Code not available. doi:10.1002/cfg.303.
Jones, Susan, and Thornton, Janet M. Wed . "Protein–DNA Interactions: The Story so Far and a New Method for Prediction". Country unknown/Code not available. doi:10.1002/cfg.303.
@article{osti_1198266,
title = {Protein–DNA Interactions: The Story so Far and a New Method for Prediction},
author = {Jones, Susan and Thornton, Janet M.},
abstractNote = {This review describes methods for the prediction of DNA binding function, and specifically summarizes a new method using 3D structural templates. The new method features the HTH motif that is found in approximately one-third of DNAbinding protein families. A library of 3D structural templates of HTH motifs was derived from proteins in the PDB. Templates were scanned against complete protein structures and the optimal superposition of a template on a structure calculated. Significance thresholds in terms of a minimum root mean squared deviation (rmsd) of an optimal superposition, and a minimum motif accessible surface area (ASA), have been calculated. In this way, it is possible to scan the template library against proteins of unknown function to make predictions about DNA-binding functionality.},
doi = {10.1002/cfg.303},
journal = {Comparative and Functional Genomics},
number = 4,
volume = 4,
place = {Country unknown/Code not available},
year = {2003},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1002/cfg.303

Citation Metrics:
Cited by: 6 works
Citation information provided by
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