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

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:
Grant/Contract Number:
FG02-96ER62166
Type:
Published Article
Journal Name:
Comparative and Functional Genomics
Additional Journal Information:
Journal Volume: 4; Journal Issue: 4; Related Information: CHORUS Timestamp: 2016-08-23 06:22:49; Journal ID: ISSN 1531-6912
Publisher:
Hindawi Publishing Corporation
Sponsoring Org:
USDOE
Country of Publication:
Country unknown/Code not available
Language:
English
OSTI Identifier:
1198266