Abstract
An important issue in understanding and classifying protein-protein interactions (PPI) is to characterize their interfaces in order to discriminate between transient and obligate complexes. We propose a classification approach to discriminate between these two types of complexes. Our approach uses contact and binding free energies of the residues present in the interaction, which are the input features for the classifiers. A total of 282 features are extracted for each complex, and the classification is performed via recently proposed dimensionality reduction (LDR) methods, including the well-know Fisher’s discriminant analysis and two heteroscedastic approaches. The results on a standard benchmark of transient and obligate protein complexes show that LDR approaches achieve a very high classification accuracy (over 78%), outperforming various support vector machines and nearest-neighbor classifiers. An additional insight on the proposed approach and experiments on different subsets of features shows that solvation energies can be used in the classification, leading to a performance comparable to using the full binding free energies of the interaction.
Chapter PDF
Similar content being viewed by others
References
Janin, J.: Kinetics and thermodynamics of protein-protein interactions from a structural perpective. In: Protein-Protein Recognition, p. 344. Oxford University Press, Oxford (2000)
Jones, S., Thornton, J.M.: Analysis and classification of protein-protein interactions from a structural perspective. In: Protein-Protein Recognition. Oxford University Press, Oxford (2000)
Russell, R.B., Alber, F., Aloy, P., Davis, F.P., Korkin, D., Pichaud, M., Topf, M., Sali, A.: A structural perspective on protein-protein interactions. Curr. Opin. Struct. Biol. 14(3), 313–324 (2004)
Kurareva, I., Abagyan, R.: Predicting molecular interactions in structural proteomics. In: Nussinov, R., Shreiber, G. (eds.) Computational Protein-Protein Interactions, pp. 185–209. CRC Press, Boca Raton (2009)
Ofran, Y.: Prediction of protein interaction sites. In: Nussinov, R., Shreiber, G. (eds.) Computational Protein-Protein Interactions, pp. 167–184. CRC Press, Boca Raton (2009)
Lawrence, M.C., Colman, P.M.: Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234(4), 946–950 (1993)
Chakrabarti, P., Janin, J.: Dissecting protein-protein recognition sites. Proteins 47(3), 334–343 (2002)
Gnatt, A.L., Cramer, P., Fu, J., Bushnell, D.A., Kornberg, R.D.: Structural basis of transcription: an RNA polymerase II elongation complex at 3. 3 A resolution. Science 292(5523), 1876–1882 (2001)
Xu, D., Tsai, C., Nussinov, R.: Hydrogen bonds and salt bridges accross protein-protein interfaces. Protein Eng. 10(9), 999–1012 (1997)
Shanahan, H., Thornton, J.: Amino acid architecture and the distribution of polar atoms on the surfaces of proteins. Biopolymers 78(6), 318–328 (2005)
Ma, B., Elkayam, T., Wolfson, H.: Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc. Natl. Acad. Sci., USA 100(10), 5772–5777 (2003)
Ofran, Y., Rost, B.: Analysing six types of protein-protein interfaces. J. Mol. Biol. 325(2), 377–387 (2003)
Nooren, I., Thornton, J.: Diversity of protein-protein interactions. EMBO Journal 22(14), 3846–3892 (2003)
Jones, S., Thornton, J.M.: Principles of protein-protein interactions. Proc. Natl Acad. Sci, USA 93(1), 13–20 (1996)
Glaser, F., Steinberg, D.M., Vakser, I.A., Ben-Tal, N.: Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 43(2), 89–102 (2001)
Zhu, H., Domingues, F., Sommer, I., Lengauer, T.: Noxclass: Prediction of protein-protein interaction types. BMC Bioinformatics 7(27) (2006) doi:10.1186/1471–2105–7–27
Young, J.: A role for surface hydrophobicity in protein protein recognition. Protein Sci. 3, 717–729 (1994)
LoConte, L., Chothia, C., Janin, J.: The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285(5), 2177–2198 (1999)
Qi, Y., Bar-Joseph, Z., Klein-Seetharaman, J.: Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins 63(3), 490–500 (2006)
Bordner, A.J., Abagyan, R.: Statistical analysis and prediction of protein-protein interfaces. Proteins 60(3), 353–366 (2005)
Caffrey, H.J., Somaroo, S.: Are protein protein interfaces more conserved in sequence than the rest of the protein surface? Protein Science 13, 190–202 (2004)
Neuvirth, S., Raz, R.: ProMate. a structure based prediction program to identify the location of protein protein binding sites. J. Mol. Biol. 338, 181–199 (2004)
Zhou, H., Shan, Y.: Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 44(3), 336–343 (2001)
Park, S.H., Reyes, J., Gilbert, D., Kim, J.W., Kim, S.: Prediction of protein-protein interaction types using association rule based classification. BMC Bioinformatics 10(36) (2009) doi:10.1186/1471-2105-10-36
Mintseris, J., Weng, Z.: Structure, function, and evolution of transient and obligate protein-protein interactions. Proc. Natl. Acad. Sci., USA 102(31), 10930–10935 (2005)
Berman, H., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T., Weissig, H., Shindyalov, I., Bourne, P.: The Protein Data Bank. Nucleic Acids Research 28, 235–242 (2000)
Rueda, L., Herrera, M.: Linear Dimensionality Reduction by Maximizing the Chernoff Distance in the Transformed Space. Pattern Recognition 41(10), 3138–3152 (2008)
Duda, R., Hart, P., Stork, D.: Pattern Classification, 2nd edn. John Wiley and Sons, Inc., New York (2000)
Fisher, R.: The Use of Multiple Measurements in Taxonomic Problems. Annals of Eugenics 7, 179–188 (1936)
Loog, M., Duin, P.: Linear Dimensionality Reduction via a Heteroscedastic Extension of LDA: The Chernoff Criterion. IEEE Transactions on Pattern Analysis and Machine Intelligence 26(6), 732–739 (2004)
Ivanciuc, O.: Applications of Support Vector Machines in Chemistry. In: Reviews in Computational Chemistry, pp. 291–400. Wiley, Chichester (2007)
Camacho, C., Zhang, C.: FastContact: rapid estimate of contact and binding free energies. Bioinformatics 21(10), 2534–2536 (2005)
Theodoridis, S., Koutroumbas, K.: Pattern Recognition, 3rd edn. Elsevier Academic Press, Amsterdam (2006)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Rueda, L., Garate, C., Banerjee, S., Mominul Aziz, M. (2010). Biological Protein-Protein Interaction Prediction Using Binding Free Energies and Linear Dimensionality Reduction. In: Dijkstra, T.M.H., Tsivtsivadze, E., Marchiori, E., Heskes, T. (eds) Pattern Recognition in Bioinformatics. PRIB 2010. Lecture Notes in Computer Science(), vol 6282. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16001-1_33
Download citation
DOI: https://doi.org/10.1007/978-3-642-16001-1_33
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-16000-4
Online ISBN: 978-3-642-16001-1
eBook Packages: Computer ScienceComputer Science (R0)