Prediction of protein-protein interaction sites using patch-based residue characterization. (English) Zbl 1307.92088
Summary: Identifying protein-protein interaction sites provides important clues to the function of a protein and is becoming increasingly relevant in topics such as systems biology and drug discovery. Using a patch-based model for residue characterization, we trained random forest classifiers for residue-based interface prediction, which was followed by a clustering procedure to produce patches for patch-based interface prediction. For residue-based interface prediction, our method achieves a specificity rate of 0.7 and a sensitivity rate of 0.78. For patch-based interface prediction, a success rate of 0.80 is achieved. Based on same datasets, we also compare it with several published methods. The results show that our method is a successful predictor for residue-based and patch-based interface prediction.
MSC:
| 92C40 | Biochemistry, molecular biology |
Software:
Cell-PLoc; GPCR-2L; GPCR-CA; Euk-mPLoc; iLoc-Virus; PSAIA; iLoc-Euk; Plant-mPLoc; AFP-Pred; GPCR-GIA; Quat-2L; SecretP; NR-2LReferences:
| [1] | Abagyan, R., Protein structure prediction by global energy optimization, (van Gunsteren, W. F., Computer Simulations of Biomolecular Systems, vol. 3 (1997), Kluwer Academic Publisher: Kluwer Academic Publisher Dordrecht), 32 |
| [2] | Andraos, J., Kinetic plasticity and the determination of product ratios for kinetic schemes leading to multiple products without rate laws: new methods based on directed graphs, Can. J. Chem., 86, 342-357 (2008) |
| [3] | Bahar, I.; Atilgan, A. R.; Erman, B., Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential, Fold. Des., 2, 173-181 (1997) |
| [4] | Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E., The Protein data bank, Nucleic Acids Res., 28, 235-242 (2000) |
| [5] | Bordner, A. J.; Abagyan, R., Statistical analysis and prediction of protein-protein interfaces, Proteins, 60, 353-366 (2005) |
| [6] | Bradford, J. R.; Needham, C. J.; Bulpitt, A. J.; Westhead, D. R., Insights into protein-protein interfaces using a Bayesian network prediction method, J. Mol. Biol., 362, 365-386 (2006) |
| [7] | Bradford, J. R.; Westhead, D. R., Improved prediction of protein-protein binding sites using a support vector machines approach, Bioinformatics, 21, 1487-1494 (2005) |
| [8] | Breiman, L., Random forests, Mach. Learn., 45, 5-32 (2001) · Zbl 1007.68152 |
| [9] | Chelliah, V.; Blundell, T. L.; Fernández-Recio, J., Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment, J. Mol. Biol., 357, 1669-1682 (2006) |
| [10] | Chen, C.; Chen, L.; Zou, X.; Cai, P., Prediction of protein secondary structure content by using the concept of Chou’s pseudo amino acid composition and support vector machine, Protein Pept. Lett., 16, 27-31 (2009) |
| [11] | Chen, H. L.; Zhou, H. X., Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data, Proteins, 61, 21-35 (2005) |
| [12] | Chen, X. W.; Jeong, J. C., Sequence-based prediction of protein interaction sites with an integrative method, Bioinformatics, 25, 585-591 (2009) |
| [13] | Chou, K. C., Review: low-frequency collective motion in biomacromolecules and its biological functions, Biophys. Chem., 30, 3-48 (1988) |
| [14] | Chou, K. C., Graphic rules in steady and non-steady enzyme kinetics, J. Biol. Chem., 264, 12074-12079 (1989) |
| [15] | Chou, K. C., Low-frequency resonance and cooperativity of hemoglobin, Trends Biochem. Sci., 14, 212 (1989) |
| [16] | Chou, K. C., A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space, Proteins, 21, 319-344 (1995) |
| [17] | Chou, K. C., Prediction of protein cellular attributes using pseudo amino acid composition, Proteins, 43, 246-255 (2001), (Erratum: Proteins, 2001, 44, 60) |
| [18] | Chou, K. C., Graphic rule for drug metabolism systems, Curr. Drug Metab., 11, 369-378 (2010) |
| [19] | Chou, K. C., Some remarks on protein attribute prediction and pseudo amino acid composition (50th Anniversary Year Review), J. Theor. Biol., 273, 236-247 (2011) · Zbl 1405.92212 |
| [20] | Chou, K. C.; Cai, Y. D., Predicting protein-protein interactions from sequences in a hybridization space, J. Proteome Res., 5, 316-322 (2006) |
| [21] | Chou, K. C.; Shen, H. B., Review: recent progresses in protein subcellular location prediction, Anal. Biochem., 370, 1-16 (2007) |
| [22] | Chou, K. C.; Shen, H. B., Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites, J. Proteome Res., 6, 1728-1734 (2007) |
| [23] | Chou, K. C.; Shen, H. B., Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms (updated version: Cell-PLoc 2.0: an improved package of web-servers for predicting subcellular localization of proteins in various organisms. Natural Science, 2010, 2, 1090-1103), Nat. Protocols, 3, 153-162 (2008) |
| [24] | Chou, K. C.; Shen, H. B., Review: recent advances in developing web-servers for predicting protein attributes, Nat. Sci., 2, 63-92 (2009) |
| [25] | Chou, K. C.; Shen, H. B., Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization, PLoS ONE, 5, e11335 (2010) |
| [26] | Chou, K. C.; Wu, Z. C.; Xiao, X., iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins, PLoS One, 6, e18258 (2011) |
| [27] | Chou, K. C.; Zhang, C. T., Review: prediction of protein structural classes, Crit. Rev. Biochem. Mol. Biol., 30, 275-349 (1995) |
| [28] | Chou, K. C.; Zhou, G. P., Role of the protein outside active site on the diffusion-controlled reaction of enzyme, J. Am. Chem. Soc., 104, 1409-1413 (1982) |
| [29] | Chung, J. L.; Wang, W.; Bourne, P. E., Exploiting sequence and structure homologs to identify protein-protein binding sites, Proteins, 62, 630-640 (2006) |
| [30] | de Vries, S. J.; Bonvin, A. M.J. J., How proteins get in touch: interface prediction in the study of biomolecular complexes, Curr. Protein Pept. Sci., 9, 394-406 (2008) |
| [31] | de Vries, S. J.; van Dijk, A. D.; Bonvin, A. M., WHISCY: what information does surface conservation yield? Application to data-driven docking, Proteins, 63, 479-489 (2006) |
| [32] | Ding, H.; Luo, L.; Lin, H., Prediction of cell wall lytic enzymes using Chou’s amphiphilic pseudo amino acid composition, Protein Pept. Lett., 16, 351-355 (2009) |
| [33] | Dong, Q. W.; Wang, X. L.; Lin, L.; Guan, Y., Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins, BMC Bioinf., 8, 147 (2007) |
| [34] | Esmaeili, M.; Mohabatkar, H.; Mohsenzadeh, S., Using the concept of Chou’s pseudo amino acid composition for risk type prediction of human papillomaviruses, J. Theor. Biol., 263, 203-209 (2010) · Zbl 1406.92455 |
| [35] | Fariselli, P.; Pazos, F.; Valencia, A.; Casadio, R., Prediction of protein-protein interaction sites in heterocomplexes with neural networks, Eur. J. Biochem., 269, 1356-1361 (2002) |
| [36] | Fauchere, J. L.; Pliska, V., Hydrophobic parameters-pi of amino-acid side-chains from the partitioning of n-acetyl-amino-acid amides, Eur. J. Med. Chem., 18, 369-375 (1983) |
| [37] | Fernandez-Recio, J.; Totrov, M.; Abagyan, R., Identification of protein-protein interaction sites from docking energy landscapes, J. Mol. Biol., 335, 843-865 (2004) |
| [38] | Georgiou, D. N.; Karakasidis, T. E.; Nieto, J. J.; Torres, A., Use of fuzzy clustering technique and matrices to classify amino acids and its impact to Chou’s pseudo amino acid composition, J. Theor. Biol., 257, 17-26 (2009) · Zbl 1400.92393 |
| [39] | Gu, Q.; Ding, Y. S.; Zhang, T. L., Prediction of G-protein-coupled receptor classes in low homology using Chou’s pseudo amino acid composition with approximate entropy and hydrophobicity patterns, Protein Pept. Lett., 17, 559-567 (2010) |
| [40] | Heuser, P.; Bau, D.; Benkert, P.; Schomburg, D., Refinement of unbound protein docking studies using biological knowledge, Proteins, 61, 1059-1067 (2005) |
| [41] | Higa, R. H.; Tozzi, C. L., A simple and efficient method for predicting protein-protein interaction sites, Genet. Mol. Res., 7, 898-909 (2008) |
| [42] | He, Z.; Zhang, J.; Shi, X. H.; Hu, L. L.; Kong, X.; Cai, Y. D.; Chou, K. C., Predicting drug-target interaction networks based on functional groups and biological features, PLoS ONE, 5, e9603 (2010) |
| [43] | Hu, L.; Huang, T.; Shi, X.; Lu, W. C.; Cai, Y. D.; Chou, K. C., Predicting functions of proteins in mouse based on weighted protein-protein interaction network and protein hybrid properties, PLoS ONE, 6, e14556 (2011) |
| [44] | Huang, T.; Shi, X. H.; Wang, P.; He, Z.; Feng, K. Y.; Hu, L.; Kong, X.; Li, Y. X.; Cai, Y. D.; Chou, K. C., Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks, PLoS ONE, 5, e10972 (2010) |
| [45] | Jia, S. C.; Hu, X. Z., Using random forest algorithm to predict beta-hairpin motifs, Protein Pept. Lett., 18, 609-617 (2011) |
| [46] | Jones, S.; Thornton, J. M., Prediction of protein-protein interaction sites using patch analysis, J. Mol. Biol., 272, 133-143 (1997) |
| [47] | Kabsch, W.; Sander, C., Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, 22, 2577-2637 (1983) |
| [48] | Kandaswamy, K. K.; Chou, K. C.; Martinetz, T.; Moller, S.; Suganthan, P. N.; Sridharan, S.; Pugalenthi, G., AFP-Pred: a random forest approach for predicting antifreeze proteins from sequence-derived properties, J. Theor. Biol., 270, 56-62 (2011) |
| [49] | Koike, A.; Takagi, T., Prediction of protein-protein interaction sites using support vector machines, Protein Eng. Des. Sel., 17, 165-173 (2004) |
| [50] | Kufareva, I.; Budagyan, L.; Raush, E.; Totrov, M.; Abagyan, R., PIER: protein interface recognition for structural proteomics, Proteins, 67, 400-417 (2007) |
| [51] | Kyte, J.; Doolittle, R. F., A simple method for displaying the hydropathic character of a protein, J. Mol. Biol., 157, 105-132 (1982) |
| [52] | Li, J. J.; Huang, D. S.; Wang, B.; Chen, P., Identifying protein-protein interfacial residues in heterocomplexes using residue conservation scores, Int. J. Biol. Macromol., 38, 241-247 (2006) |
| [53] | Liang, S. D.; Zhang, C.; Liu, S.; Zhou, Y., Protein binding site prediction using an empirical scoring function, Nucleic Acids Res., 34, 3698-3707 (2006) |
| [54] | Lin, H., The modified Mahalanobis discriminant for predicting outer membrane proteins by using Chou’s pseudo amino acid composition, J. Theor. Biol., 252, 350-356 (2008) · Zbl 1398.92076 |
| [55] | Lin, W. Z.; Xiao, X.; Chou, K. C., GPCR-GIA: a web-server for identifying G-protein coupled receptors and their families with grey incidence analysis, Protein Eng. Des. Sel., 22, 699-705 (2009) |
| [56] | Madkan, A.; Blank, M.; Elson, E.; Chou, K. C.; Geddis, M. S.; Goodman, R., Steps to the clinic with ELF EMF, Nat. Sci., 1, 157-165 (2009) |
| [57] | Mihel, J.; Sikic, M.; Tomić, S.; Jeren, B.; Vlahovicek, K., PSAIA—Protein structure and interaction analyzer, BMC Struct. Biol., 8, 21 (2008) |
| [58] | Mohabatkar, H., Prediction of cyclin proteins using Chou’s pseudo amino acid composition, Protein Pept. Lett., 17, 1207-1214 (2010) |
| [59] | Mohabatkar, H.; Mohammad Beigi, M.; Esmaeili, A., Prediction of GABA(A) receptor proteins using the concept of Chou’s pseudo-amino acid composition and support vector machine, J. Theor. Biol., 281, 18-23 (2011) · Zbl 1397.92215 |
| [60] | Neuvirth, H.; Raz, R.; Schreiber, G., ProMate: a structure based prediction program to identify the location of protein-protein binding sites, J. Mol. Biol., 338, 181-199 (2004) |
| [61] | Ofran, Y.; Rost, B., Predicted protein-protein interaction sites from local sequence information, FEBS Lett., 544, 236-239 (2003) |
| [62] | Ofran, Y.; Rost, B., ISIS: interaction sites identified from sequence, Bioinformatics, 23, E13-E16 (2007) |
| [63] | Pettit, F. K.; Bare, E.; Tsai, A.; Bowie, J. U., HotPatch: a statistical a pproach to finding biologically relevant features on protein surfaces, J. Mol. Biol., 369, 863-879 (2007) |
| [64] | Porollo, A.; Meller, J., Prediction-based fingerprints of protein-protein interactions, Proteins, 66, 630-645 (2007) |
| [65] | Qin, S. B.; Zhou, H. X., A holistic approach to protein docking, Proteins, 69, 743-749 (2007) |
| [66] | Qiu, J. D.; Huang, J. H.; Shi, S. P.; Liang, R. P., Using the concept of Chou’s pseudo amino acid composition to predict enzyme family classes: an approach with support vector machine based on discrete wavelet transform, Protein Pept. Lett., 17, 715-722 (2010) |
| [67] | Qiu, Z. J.; Wang, X. C., Identification of ligand-binding pockets in proteins using residue preference methods, Protein Pept. Lett., 16, 984-990 (2009) |
| [68] | Ren, L. H.; Shen, Y. Z.; Ding, Y. S.; Chou, K. C., Bio-entity network for analysis of protein-protein interaction networks, Asian J. Control, 13, 726-737 (2011) · Zbl 1303.93030 |
| [69] | Res, I.; Mihalek, I.; Lichtarge, O., An evolution based classifier for prediction of protein interfaces without using protein structures, Bioinformatics, 21, 2496-2501 (2005) |
| [70] | Sanner, M. F.; Olson, A. J.; Spehner, J. C., Reduced surface: an efficient way to compute molecular surfaces, Biopolymers, 38, 305-320 (1996) |
| [71] | Sikic, M.; Tomic, S.; Vlahovicek, K., Prediction of protein-protein interaction sites in sequences and 3D structures by random forests, PLoS Comput. Biol., 5, e1000278 (2009) |
| [72] | Tjong, H.; Qin, S.; Zhou, H. X., PI2PE: protein interface/interior prediction engine, Nucleic Acids Res., 35, W357-W362 (2007) |
| [73] | Tress, M.; de Juan, D.; Graña, O.; Gómez, M. J.; Gómez-Puertas, P.; González, J. M.; López, G.; Valencia, A., Scoring docking models with evolutionary information, Proteins, 60, 275-280 (2005) |
| [74] | van Dijk, A. D.J.; de Vries, S. J.; Dominguez, C.; Chen, H.; Zhou, H. X.; Bonvin, A. M.J. J., Data-driven docking: HADDOCK’s adventures in CAPRI, Proteins, 60, 232-238 (2005) |
| [75] | Wang, B.; Chen, P.; Huang, D. S.; Li, J. J.; Lok, T. M.; Lyu, M. R., Predicting protein interaction sites from residue spatial sequence profile and evolution rate, FEBS Lett., 580, 380-384 (2006) |
| [76] | Wang, B.; Wong, H. S.; Huang, D. S., Inferring protein-protein interacting sites using residue conservation and evolutionary information, Protein Pept. Lett., 13, 999-1005 (2006) |
| [77] | Wang, P.; Xiao, X.; Chou, K. C., NR-2L: a two-level predictor for identifying nuclear receptor subfamilies based on sequence-derived features, PLoS ONE, 6, e23505 (2011) |
| [78] | Wesson, L.; Eisenberg, D., Atomic solvation parameters applied to molecular-dynamics of proteins in solution, Protein Sci., 1, 227-235 (1992) |
| [79] | Xia, J. F.; Han, K.; Huang, D. S., Sequence-based prediction of protein-protein interactions by means of rotation forest and autocorrelation descriptor, Protein Pept. Lett., 17, 137-145 (2010) |
| [80] | Xiao, X.; Wang, P.; Chou, K. C., Predicting protein structural classes with pseudo amino acid composition: an approach using geometric moments of cellular automaton image, J. Theor. Biol., 254, 691-696 (2008) · Zbl 1400.92416 |
| [81] | Xiao, X.; Lin, W. Z.; Chou, K. C., Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes, J. Comput. Chem., 29, 2018-2024 (2008) |
| [82] | Xiao, X.; Wang, P.; Chou, K. C., GPCR-CA: a cellular automaton image approach for predicting G-protein-coupled receptor functional classes, J. Comput. Chem., 30, 1414-1423 (2009) |
| [83] | Xiao, X.; Chou, K. C., Using pseudo amino acid composition to predict protein attributes via cellular automata and others approaches, Curr. Bioinf., 2011, 6, 251-260 (2011) |
| [84] | Xiao, X.; Wang, P.; Chou, K. C., GPCR-2L: predicting G protein-coupled receptors and their types by hybridizing two different modes of pseudo amino acid compositions, Mol. Biosyst., 7, 911-919 (2011) |
| [85] | Xiao, X.; Wang, P.; Chou, K. C., Quat-2L: a web-server for predicting protein quaternary structural attributes, Mol. Divers., 15, 149-155 (2011) |
| [86] | Xiao, X.; Wu, Z. C.; Chou, K. C., A multi-label classifier for predicting the subcellular localization of gram-negative bacterial proteins with both single and multiple sites, PLoS One, 6, e20592 (2011) |
| [87] | Xiao, X.; Wu, Z. C.; Chou, K. C., iLoc-Virus: a multi-label learning classifier for identifying the subcellular localization of virus proteins with both single and multiple sites, J. Theor. Biol, 284, 42-51 (2011) · Zbl 1397.92238 |
| [88] | Yan, C., Dobbs, D., Honavar, V., 2003. Identification of surface residues involved in protein-protein interaction—a support vector machine approach. In: Proceedings of the Conference on Intelligence System Design Application, pp. 53-62.; Yan, C., Dobbs, D., Honavar, V., 2003. Identification of surface residues involved in protein-protein interaction—a support vector machine approach. In: Proceedings of the Conference on Intelligence System Design Application, pp. 53-62. |
| [89] | Yang, J.; Jiang, X. F., A novel approach to predict protein-protein interactions related to Alzheimer’s disease based on complex network, Protein Pept. Lett., 17, 356-366 (2010) |
| [90] | Yu, L.; Guo, Y.; Li, Y.; Li, G.; Li, M.; Luo, J.; Xiong, W.; Qin, W., SecretP: identifying bacterial secreted proteins by fusing new features into Chou’s pseudo-amino acid composition, J. Theor. Biol., 267, 1-6 (2010) · Zbl 1410.92040 |
| [91] | Zeng, Y. H.; Guo, Y. Z.; Xiao, R. Q.; Yang, L.; Yu, L. Z.; Li, M. L., Using the augmented Chou’s pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach, J. Theor. Biol., 259, 366-372 (2009) · Zbl 1402.92193 |
| [92] | Zhang, G. Y.; Fang, B. S., Predicting the cofactors of oxidoreductases based on amino acid composition distribution and Chou’s amphiphilic pseudo amino acid composition, J. Theor. Biol., 253, 310-315 (2008) |
| [93] | Zhou, G. P., The disposition of the LZCC protein residues in wenxiang diagram provides new insights into the protein-protein interaction mechanism, J. Theor. Biol., 284, 142-148 (2011) · Zbl 1397.92245 |
| [94] | Zhou, G. P.; Deng, M. H., An extension of Chou’s graphical rules for deriving enzyme kinetic equations to system involving parallel reaction pathways, Biochem. J., 222, 169-176 (1984) |
| [95] | Zhou, H. X.; Qin, S. B., Interaction-site prediction for protein complexes: a critical assessment, Bioinformatics, 23, 2203-2209 (2007) |
| [96] | Zhou, H. X.; Shan, Y. B., Prediction of protein interaction sites from sequence profile and residue neighbor list, Proteins, 44, 336-343 (2001) |
| [97] | Zhou, X. B.; Chen, C.; Li, Z. C.; Zou, X. Y., Using Chou’s amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes, J. Theor. Biol., 248, 546-551 (2007) · Zbl 1451.92245 |
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