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


BACKGROUND
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.
Ferrer-Costa
C
C
Molecular Modelling and Bioinformatics, IRBB-Parc Cientific de Barcelona, UB, Josep Samitier, 1-5 08028 Barcelona, Catalonia, Spain.
Shanahan
H P
HP
Jones
S
S
Thornton
J M
JM
D020816:Amino Acid Motifs; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D030562:Databases, Protein; D005189:False Positive Reactions; D023281:Genomics; D019077:Helix-Turn-Helix Motifs; D020407:Internet; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D012984:Software; D055672:Static Electricity; D040681:Structural Homology, Protein
D004268:DNA-Binding Proteins; D011506:Proteins