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

      Gabdoulline, R; Eckweiler, D; Kel, A; Stegmaier, P; 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. (2012-06-11)
      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/.