for sequence based prediction

http://dnabind.szialab.org

http://lcg.rit.albany.edu/dp-bind/

for structure based prediction

http://pipe.scs.fsu.edu/displar.html

http://www.prc.boun.edu.tr/appserv/prc/dnabindprot/index.html

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

Thank you. But I had in mind some tools, where the input data will be protein structure (pdb) and concrete sequence, that this protein probably binds. Can anything be used?

don't know if this fits your search, but it takes in consideration both spatial and sequence features

http://hlt.hitsz.edu.cn:8080/PDNAsite/