Abstract
Predicting of protein-protein interaction sites (PPIs) merely are researched in a single granular space in which the correlations among different levels are neglected. In this paper, PPIs models are constructed in different granular spaces based on Quotient Space Theory. We mainly use HSSP profile and PSI-Blast profile as two features for granular space, then we use granularity synthesis theory to synthesis PPIs models from different features, finally we also improve the prediction by the number of neighboring residue. With the above method, an accuracy of 59.99% with sensitivity (68.87%), CC (0.2113), F-measure (53.12%) and specificity (47.56%) is achieved after considering different level results. We then develop a post-processing scheme to improve the prediction using the relative location of the predicted residues. Best success is then achieved with sensitivity, specificity, CC, accuracy and F-measure pegged at 74.96%, 47.87%, 0.2458, 59.63% and 54.66%, respectively. Experimental results presented here demonstrate that multi-granular method can be applied to automated identification of protein interface residues.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Bradford, J.R., Westhead, D.R.: Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 21(8), 1487–1494 (2005)
Res, I., Mihalek, I., Lichtarge, O.: An evolution based classifier for prediction of protein interfaces without using protein structures. Bioinformatic 21(10), 2496–2501 (2005)
Chen, H., Zhou, H.X.: Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins: Structure, Function, and Bioinformatics 61(1) (2005)
Li, M.H., Lin, L., Wang, X.L., Liu, T.: Protein-protein interaction site prediction based on conditional random fields. Bioinformatics 23(5), 597 (2007)
Bradford, J.R., Needham, C.J., Bulpitt, A.J., Westhead, D.R.: Insights into protein-protein interfaces using a Bayesian network prediction method. Journal of Molecular Biology 362(2), 365–386 (2006)
Sikić, M., Tomić, S., Vlahoviček, K.: Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests. PLoS Comput. Biol. 5(1), e1000278 (2009)
Du, X., Cheng, J.: Prediction of protein-protein interaction sites using granularity computing of quotient space theory. In: International conference on computer science and software engineering, vol. 1, pp. 324–328. Inst. of Elec. and Elec. Eng. Computer Society (2008)
Zhang, L.: The Quotient Space Theory of Problem Solving. Fundamenta Informaticae 59(2), 287–298 (2004)
Chang, C.-C., Lin, C.-J.: LIBSVM: a library for support vector machines (2001)
Banner, D.W., D’Arcy, A., Chne, C., Winkler, F.K., Guha, A., Konigsberg, W.H., Nemerson, Y., Kirchhofer, D.: The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor (1996)
Rodgers, A.J., Wilce, M.C.: Structure of the gamma-epsilon complex of ATP synthase. Nature Structural Biology 7(11), 1051 (2000)
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
Cheng, J., Du, X., Cheng, J. (2010). Protein Interface Residues Recognition Using Granular Computing Theory. In: Yu, J., Greco, S., Lingras, P., Wang, G., Skowron, A. (eds) Rough Set and Knowledge Technology. RSKT 2010. Lecture Notes in Computer Science(), vol 6401. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16248-0_98
Download citation
DOI: https://doi.org/10.1007/978-3-642-16248-0_98
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-16247-3
Online ISBN: 978-3-642-16248-0
eBook Packages: Computer ScienceComputer Science (R0)