3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations.

Gabdoulline, R; Eckweiler, D; Kel, A; Stegmaier, P

dc.contributor.author	Gabdoulline, R
dc.contributor.author	Eckweiler, D
dc.contributor.author	Kel, A
dc.contributor.author	Stegmaier, P
dc.date.accessioned	2012-06-19T09:08:55Z
dc.date.available	2012-06-19T09:08:55Z
dc.date.issued	2012-06-11
dc.identifier.citation	3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. 2012:notNucleic Acids Res	en_GB
dc.identifier.issn	1362-4962
dc.identifier.pmid	22693215
dc.identifier.doi	10.1093/nar/gks551
dc.identifier.uri	http://hdl.handle.net/10033/229573
dc.description.abstract	We present the webserver 3D transcription factor (3DTF) to compute position-specific weight matrices (PWMs) of transcription factors using a knowledge-based statistical potential derived from crystallographic data on protein-DNA complexes. Analysis of available structures that can be used to construct PWMs shows that there are hundreds of 3D structures from which PWMs could be derived, as well as thousands of proteins homologous to these. Therefore, we created 3DTF, which delivers binding matrices given the experimental or modeled protein-DNA complex. The webserver can be used by biologists to derive novel PWMs for transcription factors lacking known binding sites and is freely accessible at http://www.gene-regulation.com/pub/programs/3dtf/.
dc.language	ENG
dc.rights	Archived with thanks to Nucleic acids research	en_GB
dc.title	3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations.
dc.type	Article	en
dc.contributor.department	Heinrich-Heine University of Duesseldorf, Universitaetstr. 1, 40225 Duesseldorf, Helmholtz Center for Infection Research, Inhoffenstrasse 7, 38234 Braunschweig, GeneXplain GmbH, Am Exer 10 b, 38302 Wolfenbüttel, BIOBASE GmbH, Halchtersche Str. 33, 38304 Wolfenbüttel, Germany and Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Science, 10 Lavrentyev Ave, 630090 Novosibirsk, Russia.	en_GB
dc.identifier.journal	Nucleic acids research	en_GB
refterms.dateFOA	2018-06-12T22:18:55Z
html.description.abstract	We present the webserver 3D transcription factor (3DTF) to compute position-specific weight matrices (PWMs) of transcription factors using a knowledge-based statistical potential derived from crystallographic data on protein-DNA complexes. Analysis of available structures that can be used to construct PWMs shows that there are hundreds of 3D structures from which PWMs could be derived, as well as thousands of proteins homologous to these. Therefore, we created 3DTF, which delivers binding matrices given the experimental or modeled protein-DNA complex. The webserver can be used by biologists to derive novel PWMs for transcription factors lacking known binding sites and is freely accessible at http://www.gene-regulation.com/pub/programs/3dtf/.