Using structural motif templates to identify proteins with DNA binding function.

@article{citeulike:1697357, abstract = {This work describes a method for predicting DNA binding function from structure using 3-dimensional templates. Proteins that bind DNA using small contiguous helix-turn-helix (HTH) motifs comprise a significant number of all DNA-binding proteins. A structural template library of seven HTH motifs has been created from non-homologous DNA-binding proteins in the Protein Data Bank. The templates were used to scan complete protein structures using an algorithm that calculated the root mean squared deviation (rmsd) for the optimal superposition of each template on each structure, based on C(alpha) backbone coordinates. Distributions of rmsd values for known HTH-containing proteins (true hits) and non-HTH proteins (false hits) were calculated. A threshold value of 1.6 A rmsd was selected that gave a true hit rate of 88.4\% and a false positive rate of 0.7\%. The false positive rate was further reduced to 0.5\% by introducing an accessible surface area threshold value of 990 A2 per HTH motif. The template library and the validated thresholds were used to make predictions for target proteins from a structural genomics project.}, address = {EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. suej@ebi.ac.uk}, author = {Jones, S. and Barker, J. A. and Nobeli, I. and Thornton, J. M. }, citeulike-article-id = {1697357}, doi = {10.1093/nar/gkg386}, issn = {1362-4962}, journal = {Nucleic Acids Res}, keywords = {protein-dna\_interaction}, month = {June}, number = {11}, pages = {2811--2823}, posted-at = {2007-09-26 14:57:22}, priority = {2}, title = {Using structural motif templates to identify proteins with DNA binding function.}, url = {http://dx.doi.org/10.1093/nar/gkg386}, volume = {31}, year = {2003} }

TY - JOUR ID - citeulike:1697357 L3 - citeulike-article-id:1697357 TI - Using structural motif templates to identify proteins with DNA binding function. JF - Nucleic Acids Res VL - 31 IS - 11 SP - 2811 EP - 2823 AD - EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. suej@ebi.ac.uk SN - 1362-4962 N2 - This work describes a method for predicting DNA binding function from structure using 3-dimensional templates. Proteins that bind DNA using small contiguous helix-turn-helix (HTH) motifs comprise a significant number of all DNA-binding proteins. A structural template library of seven HTH motifs has been created from non-homologous DNA-binding proteins in the Protein Data Bank. The templates were used to scan complete protein structures using an algorithm that calculated the root mean squared deviation (rmsd) for the optimal superposition of each template on each structure, based on C(alpha) backbone coordinates. Distributions of rmsd values for known HTH-containing proteins (true hits) and non-HTH proteins (false hits) were calculated. A threshold value of 1.6 A rmsd was selected that gave a true hit rate of 88.4% and a false positive rate of 0.7%. The false positive rate was further reduced to 0.5% by introducing an accessible surface area threshold value of 990 A2 per HTH motif. The template library and the validated thresholds were used to make predictions for target proteins from a structural genomics project. KW - protein-dna_interaction AU - Jones, S AU - Barker, JA AU - Nobeli, I AU - Thornton, JM PY - 2003/06/01/ UR - http://dx.doi.org/10.1093/nar/gkg386 ER -