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Volumn 82, Issue 9, 2014, Pages 2088-2096

Feature selection and classification of protein-protein complexes based on their binding affinities using machine learning approaches

Author keywords

Binding affinity; Discrimination; Feature selection; Machine learning techniques; Protein protein interactions

Indexed keywords

AMINO ACID; LIGAND; PROTEIN; PROTEIN PROTEIN COMPLEX; UNCLASSIFIED DRUG; MULTIPROTEIN COMPLEX; PROTEIN BINDING;

EID: 84906310378     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24564     Document Type: Article
Times cited : (37)

References (66)
  • 1
    • 0030028728 scopus 로고    scopus 로고
    • Principles of protein-protein interactions
    • Jones S, Thornton JM. Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996;93:13-20.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 13-20
    • Jones, S.1    Thornton, J.M.2
  • 2
    • 0041312697 scopus 로고    scopus 로고
    • Diversity of protein-protein interactions
    • Nooren IM, Thornton JM. Diversity of protein-protein interactions. EMBO J 2003;22:3486-3492.
    • (2003) EMBO J , vol.22 , pp. 3486-3492
    • Nooren, I.M.1    Thornton, J.M.2
  • 5
    • 1042275583 scopus 로고    scopus 로고
    • A dissection of specific and non-specific protein-protein interfaces
    • Bahadur RP, Chakrabarti P, Rodier F, Janin J. A dissection of specific and non-specific protein-protein interfaces. J Mol Biol 2004;336:943-955.
    • (2004) J Mol Biol , vol.336 , pp. 943-955
    • Bahadur, R.P.1    Chakrabarti, P.2    Rodier, F.3    Janin, J.4
  • 7
    • 72949113228 scopus 로고    scopus 로고
    • Energy based approach for understanding the recognition mechanism in protein-protein complexes
    • Gromiha MM, Yokota K, Fukui K. Energy based approach for understanding the recognition mechanism in protein-protein complexes. Mol Biosyst 2009;5:1779-1786.
    • (2009) Mol Biosyst , vol.5 , pp. 1779-1786
    • Gromiha, M.M.1    Yokota, K.2    Fukui, K.3
  • 8
    • 0031565725 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using patch analysis
    • Jones S, Thornton JM. Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 1997;272:133-143.
    • (1997) J Mol Biol , vol.272 , pp. 133-143
    • Jones, S.1    Thornton, J.M.2
  • 9
    • 1842526090 scopus 로고    scopus 로고
    • ProMate: a structure based prediction program to identify the location of protein-protein binding sites
    • Neuvirth H, Raz R, Schreiber G. ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 2004;338:181-199.
    • (2004) J Mol Biol , vol.338 , pp. 181-199
    • Neuvirth, H.1    Raz, R.2    Schreiber, G.3
  • 10
    • 1542390499 scopus 로고    scopus 로고
    • Identification of protein-protein interaction sites from docking energy landscapes
    • Fernandez-Recio J, Totrov M, Abagyan R. Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 2004;335:843-865.
    • (2004) J Mol Biol , vol.335 , pp. 843-865
    • Fernandez-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 11
    • 10844235653 scopus 로고    scopus 로고
    • Optimal docking area: a new method for predicting protein-protein interaction sites
    • Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R. Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins 2005;58:134-143.
    • (2005) Proteins , vol.58 , pp. 134-143
    • Fernandez-Recio, J.1    Totrov, M.2    Skorodumov, C.3    Abagyan, R.4
  • 12
    • 83555177311 scopus 로고    scopus 로고
    • A novel method for protein-protein interaction site prediction using phylogenetic substitution models
    • La D, Kihara D. A novel method for protein-protein interaction site prediction using phylogenetic substitution models. Proteins 2012;80:126-141.
    • (2012) Proteins , vol.80 , pp. 126-141
    • La, D.1    Kihara, D.2
  • 13
    • 84875868591 scopus 로고    scopus 로고
    • Predicting permanent and transient protein-protein interfaces
    • La D, Kong M, Hoffman W, Choi YI, Kihara D. Predicting permanent and transient protein-protein interfaces. Proteins 2013;81:805-818.
    • (2013) Proteins , vol.81 , pp. 805-818
    • La, D.1    Kong, M.2    Hoffman, W.3    Choi, Y.I.4    Kihara, D.5
  • 14
    • 0038356582 scopus 로고    scopus 로고
    • Predict protein-protein interaction sites from local sequence information
    • Ofran Y, Rost B. Predict protein-protein interaction sites from local sequence information. FEBS Lett 2003;544:236-239.
    • (2003) FEBS Lett , vol.544 , pp. 236-239
    • Ofran, Y.1    Rost, B.2
  • 15
    • 33846662784 scopus 로고    scopus 로고
    • ISIS: interaction sites identified from sequence
    • Ofran Y, Rost B. ISIS: interaction sites identified from sequence. Bioinformatics 2007;23:e13-e16.
    • (2007) Bioinformatics , vol.23
    • Ofran, Y.1    Rost, B.2
  • 16
    • 83355170696 scopus 로고    scopus 로고
    • Partner-aware prediction of interacting residues in protein-protein complexes from sequence data
    • Ahmad S, Mizuguchi K. Partner-aware prediction of interacting residues in protein-protein complexes from sequence data. PLoS One 2011;6:e29104.
    • (2011) PLoS One , vol.6
    • Ahmad, S.1    Mizuguchi, K.2
  • 17
    • 34247586171 scopus 로고    scopus 로고
    • Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners
    • Shoemaker BA, Panchenko AR. Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. Plos Comput Biol 2007;3:595-601.
    • (2007) Plos Comput Biol , vol.3 , pp. 595-601
    • Shoemaker, B.A.1    Panchenko, A.R.2
  • 18
    • 79956188706 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces
    • Tuncbag N, Gursoy A, Keskin O. Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces. Phys Biol 2011;8:035006.
    • (2011) Phys Biol , vol.8 , pp. 035006
    • Tuncbag, N.1    Gursoy, A.2    Keskin, O.3
  • 19
    • 13444262436 scopus 로고    scopus 로고
    • Predicting protein-protein interactions using signature products
    • Martin S, Roe D, Faulon JL. Predicting protein-protein interactions using signature products. Bioinformatics 2005;21:218-226.
    • (2005) Bioinformatics , vol.21 , pp. 218-226
    • Martin, S.1    Roe, D.2    Faulon, J.L.3
  • 20
    • 77957356489 scopus 로고    scopus 로고
    • Large-scale prediction of human protein-protein interactions from amino acid sequence based on latent topic features
    • Pan XY, Zhang YN, Shen HB. Large-scale prediction of human protein-protein interactions from amino acid sequence based on latent topic features. J Proteome Res 2010;9:4992-5001.
    • (2010) J Proteome Res , vol.9 , pp. 4992-5001
    • Pan, X.Y.1    Zhang, Y.N.2    Shen, H.B.3
  • 21
    • 79958028560 scopus 로고    scopus 로고
    • Adaptive compressive learning for prediction of protein-protein interactions from primary sequence
    • Zhang YN, Pan XY, Huang Y, Shen HB. Adaptive compressive learning for prediction of protein-protein interactions from primary sequence. J Theor Biol 2011;283:44-52.
    • (2011) J Theor Biol , vol.283 , pp. 44-52
    • Zhang, Y.N.1    Pan, X.Y.2    Huang, Y.3    Shen, H.B.4
  • 22
    • 0028926048 scopus 로고
    • Protein-protein interactions: methods for detection and analysis
    • Phizicky EM, Fields S. Protein-protein interactions: methods for detection and analysis. Microbiol Rev 1995;59:94-123.
    • (1995) Microbiol Rev , vol.59 , pp. 94-123
    • Phizicky, E.M.1    Fields, S.2
  • 26
    • 78650412802 scopus 로고    scopus 로고
    • The protein information and property explorer 2: gaggle-like exploration of biological proteomic data within one webpage
    • Ramos H, Shannon P, Brusniak MY, Kusebauch U, Moritz RL, Aebersold R. The protein information and property explorer 2: gaggle-like exploration of biological proteomic data within one webpage. Proteomics 2001;11:154-158.
    • (2001) Proteomics , vol.11 , pp. 154-158
    • Ramos, H.1    Shannon, P.2    Brusniak, M.Y.3    Kusebauch, U.4    Moritz, R.L.5    Aebersold, R.6
  • 27
    • 79958064379 scopus 로고    scopus 로고
    • Challenges for the prediction of macromolecular interactions
    • Wass MN, David A, Sternberg MJ. Challenges for the prediction of macromolecular interactions. Curr Opin Struct Biol 2011;21:382-390.
    • (2011) Curr Opin Struct Biol , vol.21 , pp. 382-390
    • Wass, M.N.1    David, A.2    Sternberg, M.J.3
  • 28
    • 84872225092 scopus 로고    scopus 로고
    • On the binding affinity of macromolecular interactions: daring to ask why proteins interact
    • Kastritis PL, Bonvin AMJJ. On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface 2013;10:20120835.
    • (2013) J R Soc Interface , vol.10 , pp. 20120835
    • Kastritis, P.L.1    Bonvin, A.M.J.J.2
  • 29
    • 0027087369 scopus 로고
    • Calculation of the free energy of association for protein complexes
    • Horton N, Lewis M. Calculation of the free energy of association for protein complexes. Protein Sci 1992;1:169-181.
    • (1992) Protein Sci , vol.1 , pp. 169-181
    • Horton, N.1    Lewis, M.2
  • 30
    • 0036699164 scopus 로고    scopus 로고
    • A fast empirical approach to binding free energy calculations based on protein interface information
    • Ma XH, Wang CX, Li CH, Chen WZ. A fast empirical approach to binding free energy calculations based on protein interface information. Protein Eng 2002;15:677-681.
    • (2002) Protein Eng , vol.15 , pp. 677-681
    • Ma, X.H.1    Wang, C.X.2    Li, C.H.3    Chen, W.Z.4
  • 31
    • 34547614501 scopus 로고    scopus 로고
    • A novel empirical free energy function that explains and predicts protein-protein binding affinities
    • Audie J, Scarlata S. A novel empirical free energy function that explains and predicts protein-protein binding affinities. Biophys Chem 2007;129:198-211.
    • (2007) Biophys Chem , vol.129 , pp. 198-211
    • Audie, J.1    Scarlata, S.2
  • 32
    • 0036467249 scopus 로고    scopus 로고
    • Potential of mean force for protein-protein interaction studies
    • Jiang L, Gao Y, Mao F, Liu Z, Lai L. Potential of mean force for protein-protein interaction studies. Proteins 2002;46:190-196.
    • (2002) Proteins , vol.46 , pp. 190-196
    • Jiang, L.1    Gao, Y.2    Mao, F.3    Liu, Z.4    Lai, L.5
  • 33
    • 17144383951 scopus 로고    scopus 로고
    • A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
    • Zhang C, Liu S, Zhu Q, Zhou Y. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J Med Chem 2005;48:2325-2335.
    • (2005) J Med Chem , vol.48 , pp. 2325-2335
    • Zhang, C.1    Liu, S.2    Zhu, Q.3    Zhou, Y.4
  • 34
    • 73149095625 scopus 로고    scopus 로고
    • Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction
    • Su Y, Zhou A, Xia X, Li W, Sun Z. Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction. Protein Sci 2009;18:2550-2558.
    • (2009) Protein Sci , vol.18 , pp. 2550-2558
    • Su, Y.1    Zhou, A.2    Xia, X.3    Li, W.4    Sun, Z.5
  • 35
    • 80054900286 scopus 로고    scopus 로고
    • Protein-protein binding affinity prediction on a diverse set of structures
    • Moal IH, Agius R, Bates PA. Protein-protein binding affinity prediction on a diverse set of structures. Bioinformatics 2011;27:3002-3009.
    • (2011) Bioinformatics , vol.27 , pp. 3002-3009
    • Moal, I.H.1    Agius, R.2    Bates, P.A.3
  • 36
    • 84857428250 scopus 로고    scopus 로고
    • Prediction of protein-protein binding free energies
    • Vreven T, Hwang H, Pierce BG, Weng Z. Prediction of protein-protein binding free energies. Protein Sci 2012;21:396-404.
    • (2012) Protein Sci , vol.21 , pp. 396-404
    • Vreven, T.1    Hwang, H.2    Pierce, B.G.3    Weng, Z.4
  • 37
    • 84864750577 scopus 로고    scopus 로고
    • Structure-based prediction of protein-protein binding affinity with consideration of allosteric effect
    • Tian F, Lv Y, Yang L. Structure-based prediction of protein-protein binding affinity with consideration of allosteric effect. Amino Acids 2012;43:531-543.
    • (2012) Amino Acids , vol.43 , pp. 531-543
    • Tian, F.1    Lv, Y.2    Yang, L.3
  • 38
    • 77958482609 scopus 로고    scopus 로고
    • Identification and analysis of binding site residues in protein complexes: energy based approach
    • Gromiha MM, Selvaraj S, Jayaram B, Fukui K. Identification and analysis of binding site residues in protein complexes: energy based approach. Lecture Notes Comp Sci 2010;6215:626-633.
    • (2010) Lecture Notes Comp Sci , vol.6215 , pp. 626-633
    • Gromiha, M.M.1    Selvaraj, S.2    Jayaram, B.3    Fukui, K.4
  • 39
    • 80054029788 scopus 로고    scopus 로고
    • Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes
    • Gromiha MM, Saranya N, Selvaraj S, Jayaram B, Fukui K. Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes. Proteome Sci 2011;9:S13.
    • (2011) Proteome Sci , vol.9
    • Gromiha, M.M.1    Saranya, N.2    Selvaraj, S.3    Jayaram, B.4    Fukui, K.5
  • 40
    • 0033514432 scopus 로고    scopus 로고
    • Calcium-dependent and -independent interactions of the calmodulin-binding domain of cyclic nucleotide phosphodiesterase with calmodulin
    • Yuan T, Walsh MP, Sutherland C, Fabian H, Vogel HJ. Calcium-dependent and -independent interactions of the calmodulin-binding domain of cyclic nucleotide phosphodiesterase with calmodulin. Biochemistry 1999;38:1446-1455.
    • (1999) Biochemistry , vol.38 , pp. 1446-1455
    • Yuan, T.1    Walsh, M.P.2    Sutherland, C.3    Fabian, H.4    Vogel, H.J.5
  • 41
    • 0035958004 scopus 로고    scopus 로고
    • Energetics of target peptide binding by calmodulin reveals different modes of binding
    • Brokx RD, Lopez MM, Vogel HJ, Makhatadze GI. Energetics of target peptide binding by calmodulin reveals different modes of binding. J Biol Chem 2001;276:14083-14091.
    • (2001) J Biol Chem , vol.276 , pp. 14083-14091
    • Brokx, R.D.1    Lopez, M.M.2    Vogel, H.J.3    Makhatadze, G.I.4
  • 42
    • 77952068704 scopus 로고    scopus 로고
    • Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark
    • Kastritis PL, Bonvin AM. Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. J Proteome Res 2010;9:2216-2225.
    • (2010) J Proteome Res , vol.9 , pp. 2216-2225
    • Kastritis, P.L.1    Bonvin, A.M.2
  • 44
    • 0037474541 scopus 로고    scopus 로고
    • Structural characterisation and functional significance of transient protein-protein interactions
    • Nooren IM, Thornton JM. Structural characterisation and functional significance of transient protein-protein interactions. J Mol Biol 2003;325:991-1018.
    • (2003) J Mol Biol , vol.325 , pp. 991-1018
    • Nooren, I.M.1    Thornton, J.M.2
  • 45
    • 77957771797 scopus 로고    scopus 로고
    • Transient protein-protein interactions: structural, functional, and network properties
    • Perkins JR, Diboun I, Dessailly BH, Lees JG, Orengo C. Transient protein-protein interactions: structural, functional, and network properties. Structure 2010;18:1233-1243.
    • (2010) Structure , vol.18 , pp. 1233-1243
    • Perkins, J.R.1    Diboun, I.2    Dessailly, B.H.3    Lees, J.G.4    Orengo, C.5
  • 48
    • 18344371857 scopus 로고    scopus 로고
    • A statistical model for predicting protein folding rates from amino acid sequence with structural class information
    • Gromiha MM. A statistical model for predicting protein folding rates from amino acid sequence with structural class information. J Chem Inf Model 2005;45:494-501.
    • (2005) J Chem Inf Model , vol.45 , pp. 494-501
    • Gromiha, M.M.1
  • 49
    • 26444473604 scopus 로고    scopus 로고
    • Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure information
    • Garg A, Kaur H, Raghava GP. Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure information. Proteins 2005;61:318-324.
    • (2005) Proteins , vol.61 , pp. 318-324
    • Garg, A.1    Kaur, H.2    Raghava, G.P.3
  • 51
    • 0003120218 scopus 로고    scopus 로고
    • Fast training of support vector machines using sequential minimal optimization
    • Platt JC. Fast training of support vector machines using sequential minimal optimization. Microsoft Res 2000;12:41-65.
    • (2000) Microsoft Res , vol.12 , pp. 41-65
    • Platt, J.C.1
  • 53
    • 0041382385 scopus 로고    scopus 로고
    • Available at
    • Breiman L. Random forests. 2001. Available at: http://oz.berkeley.edu/users/breiman/randomforest2001.pdf.
    • (2001) Random forests
    • Breiman, L.1
  • 54
    • 0004060921 scopus 로고    scopus 로고
    • Correlation-based feature selection for machine learning
    • University of Waikato, Hamilton, New Zealand
    • Hall MA. Correlation-based feature selection for machine learning, PhD thesis, Department of Computer Science, University of Waikato, Hamilton, New Zealand; 1998.
    • (1998) PhD thesis, Department of Computer Science
    • Hall, M.A.1
  • 55
    • 0036161259 scopus 로고    scopus 로고
    • Gene selection for cancer classification using support vector machines
    • Guyon I, Weston J, Barnhill S, Vapnik V. Gene selection for cancer classification using support vector machines. Machine Learn 2002;46:389-422.
    • (2002) Machine Learn , vol.46 , pp. 389-422
    • Guyon, I.1    Weston, J.2    Barnhill, S.3    Vapnik, V.4
  • 57
    • 0002715112 scopus 로고    scopus 로고
    • A probabilistic approach to feature selection-a filter solution
    • Bari, Italy, July 3-6
    • Liu H, Setiono R. A probabilistic approach to feature selection-a filter solution, 13th International Conference on Machine Learning, Bari, Italy, July 3-6, 1996. pp 319-327.
    • (1996) 13th International Conference on Machine Learning , pp. 319-327
    • Liu, H.1    Setiono, R.2
  • 59
    • 0023803244 scopus 로고
    • Predicting the secondary structure of globular proteins using Neural Network models
    • Qian N, Sejnowski T. Predicting the secondary structure of globular proteins using Neural Network models. J Mol Biol 1988;202:865-884.
    • (1988) J Mol Biol , vol.202 , pp. 865-884
    • Qian, N.1    Sejnowski, T.2
  • 60
    • 0023232669 scopus 로고
    • Principal property values for six non-natural amino acids and their application to a structure-activity relationship for oxytocin peptide analogues
    • Wold S, Eriksson L, Hellberg S, Jonsson, J, Sjöström M, Skagerberg B, Wikström C. Principal property values for six non-natural amino acids and their application to a structure-activity relationship for oxytocin peptide analogues. Can J Chem 1987;65:1814-1820.
    • (1987) Can J Chem , vol.65 , pp. 1814-1820
    • Wold, S.1    Eriksson, L.2    Hellberg, S.3    Jonsson, J.4    Sjöström, M.5    Skagerberg, B.6    Wikström, C.7
  • 61
    • 0035066602 scopus 로고    scopus 로고
    • ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions
    • Thorn KS, Bogan AA. ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics 2001;17:284-285.
    • (2001) Bioinformatics , vol.17 , pp. 284-285
    • Thorn, K.S.1    Bogan, A.A.2
  • 62
    • 33644878621 scopus 로고    scopus 로고
    • PINT: protein-protein interactions thermodynamic database
    • Kumar MDS, Gromiha MM. PINT: protein-protein interactions thermodynamic database. Nucl Acids Res 2006;34:D195-D198.
    • (2006) Nucl Acids Res , vol.34
    • Kumar, M.D.S.1    Gromiha, M.M.2
  • 63
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: a protein sequence culling server
    • Wang G, Dunbrack RL, Jr. PISCES: a protein sequence culling server. Bioinformatics 2003;19:1589-1591.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 64
    • 84869068058 scopus 로고    scopus 로고
    • Binding efficiency of protein-protein complexes
    • Day ES, Cote SM, Whitty A. Binding efficiency of protein-protein complexes. Biochemistry 2012;51:9124-9136.
    • (2012) Biochemistry , vol.51 , pp. 9124-9136
    • Day, E.S.1    Cote, S.M.2    Whitty, A.3
  • 65
    • 33750999318 scopus 로고    scopus 로고
    • Disorder and sequence repeats in hub proteins and their implications for network evolution
    • Dosztanyi Z, Chen J, Dunker AK, Simon I, Tompa P. Disorder and sequence repeats in hub proteins and their implications for network evolution. J Proteome Res 2006;5:2985-2995.
    • (2006) J Proteome Res , vol.5 , pp. 2985-2995
    • Dosztanyi, Z.1    Chen, J.2    Dunker, A.K.3    Simon, I.4    Tompa, P.5
  • 66
    • 34547943482 scopus 로고    scopus 로고
    • Molecular principles of the interactions of disordered proteins
    • Mészáros B, Tompa P, Simon I, Dosztányi Z. Molecular principles of the interactions of disordered proteins. J Mol Biol 2007;372:549-561.
    • (2007) J Mol Biol , vol.372 , pp. 549-561
    • Mészáros, B.1    Tompa, P.2    Simon, I.3    Dosztányi, Z.4


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