||Nov 24, 2016
M. Michael Gromiha, Department of Biotechnology, Indian Institute of Technology Madras, India
Protein interactions: Integrating computational methods and experimental data for understanding the binding specificity
Protein-protein interactions play crucial roles in many biological processes and
responsible for smooth functioning of the machinery in living organisms.
Predicting the binding affinity of protein-protein complexes and understanding
the recognition mechanism are challenging problems in computational
and molecular biology (1).
We have developed a generalized energy based approach for identifying
the binding site residues and interacting pairs in all types of
We observed that the residues with charged and aromatic side chains
are important for binding in protein-protein complexes.
These residues influence to form cation–p, electrostatic and aromatic
Our observations have been verified with the experimental binding specificity
of protein-protein complexes and found good agreement with experiments (2).
Further, we have developed algorithms for discriminating protein-protein
complexes based on their binding affinities (3) and predicting the
binding affinity (4).
We suggest that our method would serve as an effective tool for identifying
the interacting partners in protein-protein interaction networks and
human-pathogen interactions based on the strength of interactions (5).
The salient features of the results will be discussed.
- M.M. Gromiha (2010) Protein Bioinformatics, Elsevier Publishers
- M.M. Gromiha, K. Yokota and K Fukui (2009) Mol. Biosystems 5: 1779-1786.
- K. Yugandhar and M.M. Gromiha (2014) Proteins. 82: 2088-96.
- K. Yugandhar and M.M. Gromiha (2014) Bioinformatics.30: 3583-9.
- K. Yugandhar and M.M. Gromiha (2016) Curr. Prot. Pept. Sci. 17:72-81.
- M.M. Gromiha, K. Yugandhar and S. Jemimah (2017) Curr. Opin. Str. Biol. (in press)