Email updates

Keep up to date with the latest news and content from BMC Research Notes and BioMed Central.

Open Access Open Badges Technical Note

Computational prediction of protein-protein complexes

Seema Mishra

Author Affiliations

Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, AP, India

BMC Research Notes 2012, 5:495  doi:10.1186/1756-0500-5-495

Published: 9 September 2012



Protein-protein interactions form the core of several biological processes. With protein-protein interfaces being considered as drug targets, studies on their interactions and molecular mechanisms are gaining ground. As the number of protein complexes in databases is scarce as compared to a spectrum of independent protein molecules, computational approaches are being considered for speedier model derivation and assessment of a plausible complex. In this study, a good approach towards in silico generation of protein-protein heterocomplex and identification of the most probable complex among thousands of complexes thus generated is documented. This approach becomes even more useful in the event of little or no binding site information between the interacting protein molecules.


A plausible protein-protein hetero-complex was fished out from 10 docked complexes which are a representative set of complexes obtained after clustering of 2000 generated complexes using protein-protein docking softwares. The interfacial area for this complex was predicted by two “hotspot” prediction programs employing different algorithms. Further, this complex had the lowest energy and most buried surface area of all the complexes with the same interfacial residues.


For the generation of a plausible protein heterocomplex, various software tools were employed. Prominent are the protein-protein docking methods, prediction of ‘hotspots’ which are the amino acid residues likely to be in an interface and measurement of buried surface area of the complexes. Consensus generated in their predictions lends credence to the use of the various softwares used.

Protein-protein complex prediction; Protein-protein interface; Unbound protein-protein docking; HHsearch; ZDOCK; ClusPro; MetaPPISP; Optimal docking area; Surface racer