Can anyone please suggest tools or software for predicting putative protein-protein or protein-DNA interactions?
Protein-protein interaction (PPI) networks enable us to better understand the functional organization of the proteome.
http://www.biomedcentral.com/1752-0509/3/112
you may check this software:
http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0010728
http://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction
Gaussian 09, using ONIOM for different calculation levels depending of the importance of the part to focus on.
you may use following web servers for P-P interaction
http://www.imtech.res.in/raghava/proprint/resources.html
http://www.cs.duke.edu/donaldlab/osprey.php
http://www.geneinfinity.org/sp/sp_proteininteraction.html
http://www.science.co.il/biomedical/protein-tools.asp
http://www.shodhaka.com/cgi-bin/startbioinfo/simpleresources.pl?tn=Protein-protein%20interactions%20%28all%20resources%29
I recommend ODA approach (Molsoft) and their free web based tool:
http://www.molsoft.com/oda.cgi
Indeed the new module in Schrodinger is a good alternative too. If you only wish to calculate which are the residues involved in interactions I think you are limited to these software's. However, if you want to obtain some binding mode indeed than you have to use some good protein-protein docking software as such for example HADDOCK (free) or ICM and Schrodinger. Thus, if you have some biochemical information available about the binding sites i.e. which residues are involved in the interaction you can use this information and go for protein-protein docking, if not you can identify them by ODA and then apply docking.
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