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

2.50
Hdl Handle:
http://hdl.handle.net/10033/229573
Title:
3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations.
Authors:
Gabdoulline, R; Eckweiler, D; Kel, A; Stegmaier, P
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/.
Affiliation:
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.
Citation:
3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. 2012:notNucleic Acids Res
Journal:
Nucleic acids research
Issue Date:
11-Jun-2012
URI:
http://hdl.handle.net/10033/229573
DOI:
10.1093/nar/gks551
PubMed ID:
22693215
Type:
Article
ISSN:
1362-4962
Appears in Collections:
publications of the division molecular bacteriology (MOBA)

Full metadata record

DC FieldValue Language
dc.contributor.authorGabdoulline, Ren_GB
dc.contributor.authorEckweiler, Den_GB
dc.contributor.authorKel, Aen_GB
dc.contributor.authorStegmaier, Pen_GB
dc.date.accessioned2012-06-19T09:08:55Z-
dc.date.available2012-06-19T09:08:55Z-
dc.date.issued2012-06-11-
dc.identifier.citation3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. 2012:notNucleic Acids Resen_GB
dc.identifier.issn1362-4962-
dc.identifier.pmid22693215-
dc.identifier.doi10.1093/nar/gks551-
dc.identifier.urihttp://hdl.handle.net/10033/229573-
dc.description.abstractWe 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/.en_GB
dc.languageENG-
dc.rightsArchived with thanks to Nucleic acids researchen_GB
dc.title3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations.-
dc.typeArticleen
dc.contributor.departmentHeinrich-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.journalNucleic acids researchen_GB

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