Check this list, and I feel that one of them must fit what you are looking for.

Web based tools

• PREPPI: A web service to predict protein-protein interactions by combining structural and non-structural information.

• PredUs: A tool to predict protein-protein interface based on interface conservation among structurally similar protein neighbors.

• PUDGE: This protein structure prediction server provides a convenient means of integrating tools that may be used at different stages of the structural prediction process.

• Mark-Us: A Function Annotation Server for Protein Structures.

• Target Explorer: A web based tool for automatic identification of new target genes for transcription factors in the Drosophila genome.

• EDGI: (Enhancer Detection using only Genomic Information) discovers transcriptional regulatory regions in Drosophila by a non-alignment method for phylogenetic footprinting.

• Model Quality Assessment: Global and Local Quality Assessment of Protein Models.

• STING Millennium: A web based suite of programs for comprehensive and simultaneous analysis of structure and sequence: nature and volume of atomic contacts of both intra- and inter- chain types, analysis of the quality of structure, residue conservation and its relationship with intra-chain contacts, functional parameters are also deciphered.

• SCREEN: A web server tool for identifying protein cavities and computing cavity attributes that can be applied for classification and analysis.

Thanks a ton that would surely help.

Try RoettaDock server. http://rosettadock.graylab.jhu.edu/

In the output file you can find a table of residue-residue pair energies for residues which interact across the docking interface.

I hope this can help you !!!

And another web server for docking is HADDOCK.

Can be found at http://haddock.science.uu.nl

And to add to the list, another bioinformatics prediction tools for interfaces: CPORT

http://haddock.science.uu.nl/services/CPORT

Try GRAMMX (Vakser Tool) freely available online web tool or ZDOCK

Try

Vina http://vina.scripps.edu/

PS2 http://ps2.life.nctu.edu.tw/

LigandScout

Another program is Hex http://hex.loria.fr/

Hi, have a look in this article, it contains a list of different software packages that you potentially can use to solve your question.

http://www.nature.com/nmeth/journal/v7/n3s/full/nmeth.1427.html

Just try for FlexX.. its very simple to perform