iFace: A Bioinformatics Tool for the Analysis of Protein-Protein Interface

Ganesan Pugalenthi, Govindaraju Archunan, Thennarasu Sugumar


Detailed knowledge of protein-protein interaction is essential to understand various biochemical and biological functions. In this paper, we present a bioinformatics tool to analyze the protein-protein interfaces using three-dimensional structural information. iFace identifies protein-protein interaction sites and various interactions that contribute  to the specificity and strength of the protein complex.


Protein-Protein Interactions, Protein-Protein Complex, iFace, Structural Information

Full Text:



Jones,S. and Thornton,J.M. (1995) Protein-protein interactions: a review of protein dimer structures. Prog.Biophys. Mol. Biol., 63, 31-65.

Nooren,I.M. and Thornton,J.M. (2003) Diversity of protein-protein interactions. EMBO J., 22, 3486-3492.

Ofran,Y. and Rost,B. (2003) Analysing six types of protein-protein interfaces. J. Mol. Biol., 325, 377-387.

Segal, E. et al. (2003) Discovering molecular pathways from protein interaction and gene expression data. Bioinformatics. 19 Suppl 1:i264-271.

Kann, M.G (2007). Protein interactions and disease: computational approaches to uncover the etiology of diseases. Brief Bioinform. 8(5), 333-346

David, A. et al. (2012). Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs. Hum Mutat. 33(2), 359-363

Jones, S. and Thornton, J.M. (1996) Principles of protein-protein interactions. Proc. Natl. Acad. Sci. U S A., 93, 13–20.

Kuttner, Y. Y. et al. (2011) Protein Hot Spots: The Islands of Stability. J Mol Biol. 415(2):419-428.

Bonsor, D.A. and Sundberg, E.J. (2011) Dissecting protein-protein interactions using directed evolution. Biochemistry. 50(13), 2394-2402.

Babu,M.M. (2003) NCI: A server to identify non-canonical interactions in protein structures. Nucleic Acids Res., 31, 3345-3348.

Finn, R.D. (2005) iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics. 21(3):410-412.

Pugalenthi, G. et al. (2005) DIAL: a web-based server for the automatic identification of structural domains in proteins. Nucleic Acids Res. 33(Web Server issue):W130-132.

Murakami, Y. and Jones, S. (2006) SHARP2: protein-protein interaction predictions using patch analysis. Bioinformatics. 22(14), 1794-1795.

Prieto. C. and De Las Rivas, J. (2006) APID: Agile Protein Interaction DataAnalyzer. Nucleic Acids Res. 34(Web Server issue), W298-302.

Negi,S.S. et al. (2007) InterProSurf: a web server for predicting interacting sites on protein surfaces. Bioinformatics, 23, 3397-3399.

Tina,K.G. et al. (2007) PIC: Protein Interactions Calculator. Nucleic Acids Res., 35, W473-476.

Keskin, O. and Nussinov, R. (2008) Gursoy A. PRISM: protein-protein interaction prediction by structural matching. Methods Mol Biol. 484, 505-521.

Reynolds,C. (2009) ProtorP: a protein-protein interaction analysis server. Bioinformatics, 25, 413-414.

Tuncbag,N. et al. (2010) HotPoint: hot spot prediction server for protein interfaces. Nucleic Acids Res., 38, W402-406.

Shameer, K et al. (2011) 3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. Database (Oxford). 2011,bar042.

Shin,Y.C. (2011) TRIP Database: a manually curated database of protein-protein interactions for mammalian TRP channels. Nucleic Acids Res. 39(Database issue), D356-361.

Xiaolei,Z. and Julie,C.M. (2011) KFC2: A knowledge-based hot spot prediction method based on interface solvation, atomic density and plasticity features. Proteins, 79, 2671-2683.

Krissinel, E. and Henrick, K. (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol. 372(3), 774-797.

Sundaramurthy, P. et al. (2010) HORI: aweb server to compute Higher Order Residue Interactions in protein structures. BMC Bioinformatics. 11 Suppl 1:S24

Tsai, C.J. Et al. (1996) A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J Mol Biol., 260(4), 604-620.

Pugalenthi,G. et al. (2008) Identification of catalytic residues from protein structure using support vector machine with sequence and structural features. Biochem.Biophys. Res. Commun. 367, 630-634.

Pugalenthi,G. et al. (2009) Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble. Bioinformatics, 25, 204-210.

Pugalenthi,G. et al. (2010) SMpred: a support vector machine approach to identify structural motifs in protein structure without using evolutionary information. J. Biomol. Struct.Dyn., 28, 405-414.

Mizuguchi,K. et al. (1998) JOY: protein sequence-structure representation and analysis. Bioinformatics, 14, 617-¬623.

Sowdhamini,R. et al. (1989) Stereochemical modelling of disulfide bridges: Criteria for introduction into proteins by site-directed mutagenesis. Prot. Engng., 3, 95-103.

Biro,J.C. (2006) Amino acid size, charge, hydropathy indices and matrices for protein structure analysis. Theor. Biol. Med. Model., 3, 15.

Vitagliano,L. et al. (1998) Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine. Protein Sci., 7, 1691-1699.