Tools To Predict Binding Affinity From Protein Domain Information?

Question

[Biostar User]

Are there any computational tools to predict binding affinity to specific DNA motifs from protein domain sequence information?

[Khader Shameer]

Cross-posted here http://biology.stackexchange.com/questions/2461/tools-to-predict-binding-affinity-from-protein-domain-information

Answer 1

[ff.cc.cc]

I suggest looking at interpro site (enter link description here) to get detailed information about protein domains

A popular tool for prediction of affinity should be FIMO, part of the MEME suite (http://meme.sdsc.edu):

Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, "MEME SUITE: tools for motif discovery and searching", Nucleic Acids Research, 37:W202-W208, 2009.

I found interesting suggestions also here:

A Linear Model for Transcription Factor Binding Affinity Prediction in Protein Binding Microarrays Annala M, Laurila K, Lähdesmäki H, Nykter M (2011) A Linear Model for Transcription Factor Binding Affinity Prediction in Protein Binding Microarrays. PLoS ONE 6(5): e20059. doi:10.1371/journal.pone.0020059

p.s. look also at past answers in the site

Answer 2

[zhidong.yuan]

These tools may help you to solve problems:

DR_bind server: http://dnasite.limlab.ibms.sinica.edu.tw

DBindR web server: http://www.cbi.seu.edu.cn/DBindR/DBindR.htm