Question: Tools To Predict Binding Affinity From Protein Domain Information?
2
gravatar for Biostar User
6.5 years ago by
Biostar User350
Biostar User350 wrote:

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

transcription-factor • 2.5k views
ADD COMMENTlink written 6.5 years ago by Biostar User350
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gravatar for ff.cc.cc
6.5 years ago by
ff.cc.cc1.2k
European Union
ff.cc.cc1.2k wrote:

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

ADD COMMENTlink written 6.5 years ago by ff.cc.cc1.2k
1
gravatar for zhidong.yuan
6.5 years ago by
zhidong.yuan20
United States
zhidong.yuan20 wrote:

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

ADD COMMENTlink written 6.5 years ago by zhidong.yuan20
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