Literature DB >> 16030074

HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif.

C Ferrer-Costa1, H P Shanahan, S Jones, J M Thornton.   

Abstract

SUMMARY: HTHquery is a web-based service to determine if a protein structure has a helix-turn-helix structural motif which could bind to DNA. It is based on a similarity with a set of structural templates, the accessibility of a putative structural motif and a positive electrostatic potential in the neighbourhood of the putative motif. A set of scores are computed, based on each template, using a linear predictor. From the training set used, the predictor has a true positive rate of 83.5% and a false positive rate of 0.8%. The emphasis for the website is on providing a straightforward interface which can be easily used by a bench-based scientist. AVAILABILITY: HTHquery is implemented using a set of Perl scripts and C program and can be accessed freely on the website http://www.ebi.ac.uk/thornton-srv/databases/HTHquery.

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Year:  2005        PMID： 16030074     DOI： 10.1093/bioinformatics/bti575

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  11 in total

1.  Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function.

Authors:  Huiying Zhao; Yuedong Yang; Yaoqi Zhou
Journal:  Bioinformatics       Date:  2010-06-04       Impact factor: 6.937

2.  Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes.

Authors:  Kyle E Kemege; John M Hickey; Scott Lovell; Kevin P Battaile; Yang Zhang; P Scott Hefty
Journal:  J Bacteriol       Date:  2011-09-30       Impact factor: 3.490

3.  Identification of DNA-binding proteins using structural, electrostatic and evolutionary features.

Authors:  Guy Nimrod; András Szilágyi; Christina Leslie; Nir Ben-Tal
Journal:  J Mol Biol       Date:  2009-02-20       Impact factor: 5.469

4.  A structural-alphabet-based strategy for finding structural motifs across protein families.

Authors:  Chih Yuan Wu; Yao Chi Chen; Carmay Lim
Journal:  Nucleic Acids Res       Date:  2010-06-04       Impact factor: 16.971

5.  The helix-turn-helix motif as an ultrafast independently folding domain: the pathway of folding of Engrailed homeodomain.

Authors:  Tomasz L Religa; Christopher M Johnson; Dung M Vu; Scott H Brewer; R Brian Dyer; Alan R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-18       Impact factor: 11.205

6.  DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry.

Authors:  Yao Chi Chen; Jon D Wright; Carmay Lim
Journal:  Nucleic Acids Res       Date:  2012-05-31       Impact factor: 16.971

Review 7.  An overview of the prediction of protein DNA-binding sites.

Authors:  Jingna Si; Rui Zhao; Rongling Wu
Journal:  Int J Mol Sci       Date:  2015-03-06       Impact factor: 5.923

8.  Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information.

Authors:  Wenwei Xiong; Tonghua Li; Kai Chen; Kailin Tang
Journal:  Nucleic Acids Res       Date:  2009-08-03       Impact factor: 16.971

9.  ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors.

Authors:  Wen-Yi Chu; Yu-Feng Huang; Chun-Chin Huang; Yi-Sheng Cheng; Chien-Kang Huang; Yen-Jen Oyang
Journal:  Nucleic Acids Res       Date:  2009-05-29       Impact factor: 16.971

10.  DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces.

Authors:  Harianto Tjong; Huan-Xiang Zhou
Journal:  Nucleic Acids Res       Date:  2007-02-06       Impact factor: 16.971
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