3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations
Open Access
- 11 June 2012
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 40 (W1) , W180-W185
- https://doi.org/10.1093/nar/gks551
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/.Keywords
This publication has 19 references indexed in Scilit:
- Predicting Target DNA Sequences of DNA-Binding Proteins Based on Unbound StructuresPLOS ONE, 2012
- An all‐atom, distance‐dependent scoring function for the prediction of protein–DNA interactions from structureProteins-Structure Function and Bioinformatics, 2006
- Measuring similarities between transcription factor binding sitesBMC Bioinformatics, 2005
- Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarraysNature Genetics, 2004
- Intermolecular and Intramolecular Readout Mechanisms in Protein–DNA RecognitionJournal of Molecular Biology, 2004
- MATCHTM: a tool for searching transcription factor binding sites in DNA sequencesNucleic Acids Research, 2003
- Additivity in protein-DNA interactions: how good an approximation is it?Nucleic Acids Research, 2002
- The Protein Data BankNucleic Acids Research, 2000
- Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cellsJournal of Molecular Biology, 1999
- Transcription regulatory region analysis using signal detection and fuzzy clustering.Bioinformatics, 1998