메뉴 건너뛰기




Volumn 12, Issue , 2011, Pages

Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITE PREDICTIONS; ENSEMBLE CLASSIFIERS; EVOLUTIONARY CONSERVATIONS; EXPERIMENTAL APPROACHES; PHYSICOCHEMICAL PROPERTY; PROTEIN INTERACTION; PROTEIN-BINDING SITES; SEQUENCE CONSERVATION;

EID: 80052028418     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-352     Document Type: Article
Times cited : (43)

References (38)
  • 1
    • 79954438347 scopus 로고    scopus 로고
    • Structural and docking studies of Leucaena leucocephala Cinnamoyl CoA reductase
    • Prasad NK, Vindal V, Kumar V, Kabra A, Phogat N, Kumar M. Structural and docking studies of Leucaena leucocephala Cinnamoyl CoA reductase. J Mol Model 2010, 17:533-541.
    • (2010) J Mol Model , vol.17 , pp. 533-541
    • Prasad, N.K.1    Vindal, V.2    Kumar, V.3    Kabra, A.4    Phogat, N.5    Kumar, M.6
  • 2
    • 0030028728 scopus 로고    scopus 로고
    • Principles of protein-protein interactions
    • Jones S, Thornton JM. Principles of protein-protein interactions. ProcNatlAcadSciUSA 1996, 93:13.
    • (1996) ProcNatlAcadSciUSA , vol.93 , pp. 13
    • Jones, S.1    Thornton, J.M.2
  • 3
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo CL, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. JMolBiol 1999, 285:2177.
    • (1999) JMolBiol , vol.285 , pp. 2177
    • Lo, C.L.1    Chothia, C.2    Janin, J.3
  • 4
    • 0032522670 scopus 로고    scopus 로고
    • Morphology of protein-protein interfaces
    • 10.1016/S0969-2126(98)00044-6, 9562553
    • Larsen TA, Olson AJ, Goodsell DS. Morphology of protein-protein interfaces. Structure 1998, 6:421-427. 10.1016/S0969-2126(98)00044-6, 9562553.
    • (1998) Structure , vol.6 , pp. 421-427
    • Larsen, T.A.1    Olson, A.J.2    Goodsell, D.S.3
  • 5
    • 0035342450 scopus 로고    scopus 로고
    • Residue frequencies and pairing preferences at protein-protein interfaces
    • 10.1002/1097-0134(20010501)43:2<89::AID-PROT1021>3.0.CO;2-H, 11276079
    • Glaser F, Steinberg DM, Vakser IA, Ben Tal N. Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 2001, 43:89. 10.1002/1097-0134(20010501)43:2<89::AID-PROT1021>3.0.CO;2-H, 11276079.
    • (2001) Proteins , vol.43 , pp. 89
    • Glaser, F.1    Steinberg, D.M.2    Vakser, I.A.3    Ben Tal, N.4
  • 6
    • 24344484686 scopus 로고    scopus 로고
    • Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data
    • 10.1002/prot.20514, 16080151
    • Chen H, Zhou H-X. Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins 2005, 61:21-35. 10.1002/prot.20514, 16080151.
    • (2005) Proteins , vol.61 , pp. 21-35
    • Chen, H.1    Zhou, H.-X.2
  • 7
    • 0029109468 scopus 로고
    • Protein-protein interactions: a review of protein dimer structures
    • 10.1016/0079-6107(94)00008-W, 7746868
    • Jones S, Thornton JM. Protein-protein interactions: a review of protein dimer structures. Prog Biophys Mol Biol 1995, 63:31-65. 10.1016/0079-6107(94)00008-W, 7746868.
    • (1995) Prog Biophys Mol Biol , vol.63 , pp. 31-65
    • Jones, S.1    Thornton, J.M.2
  • 8
    • 30644470508 scopus 로고    scopus 로고
    • Predicting protein interaction sites from residue spatial sequence profile and evolution rate
    • 10.1016/j.febslet.2005.11.081, 16376878
    • Wang B, Chen P, Huang D-S, Li J, Lok T-M, Lyu MR. Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett 2006, 580:380-384. 10.1016/j.febslet.2005.11.081, 16376878.
    • (2006) FEBS Lett , vol.580 , pp. 380-384
    • Wang, B.1    Chen, P.2    Huang, D.-S.3    Li, J.4    Lok, T.-M.5    Lyu, M.R.6
  • 9
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. JMolBiol 1996, 257:342.
    • (1996) JMolBiol , vol.257 , pp. 342
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 10
    • 13244292990 scopus 로고    scopus 로고
    • A two-stage classifier for identification of protein-protein interface residues
    • 10.1093/bioinformatics/bth920, 15262822
    • Yan C, Dobbs D, Honavar V. A two-stage classifier for identification of protein-protein interface residues. Bioinformatics 2004, 20(Suppl 1):i371-378. 10.1093/bioinformatics/bth920, 15262822.
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Yan, C.1    Dobbs, D.2    Honavar, V.3
  • 11
    • 0028566271 scopus 로고
    • The subunit interfaces of oligomeric enzymes are conserved to a similar extent to the overall protein sequences
    • 10.1002/pro.5560031231, 2142754, 7757001
    • Grishin NV, Phillips MA. The subunit interfaces of oligomeric enzymes are conserved to a similar extent to the overall protein sequences. Protein Sci 1994, 3:2455-2458. 10.1002/pro.5560031231, 2142754, 7757001.
    • (1994) Protein Sci , vol.3 , pp. 2455-2458
    • Grishin, N.V.1    Phillips, M.A.2
  • 12
    • 0346733329 scopus 로고    scopus 로고
    • Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
    • 10.1110/ps.03323604, 2286531, 14691234
    • Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?. Protein Sci 2004, 13:190-202. 10.1110/ps.03323604, 2286531, 14691234.
    • (2004) Protein Sci , vol.13 , pp. 190-202
    • Caffrey, D.R.1    Somaroo, S.2    Hughes, J.D.3    Mintseris, J.4    Huang, E.S.5
  • 13
    • 33747150197 scopus 로고    scopus 로고
    • Protein binding site prediction using an empirical scoring function
    • 10.1093/nar/gkl454, 1540721, 16893954
    • Liang S, Zhang C, Liu S, Zhou Y. Protein binding site prediction using an empirical scoring function. Nucleic Acids Res 2006, 34:3698-3707. 10.1093/nar/gkl454, 1540721, 16893954.
    • (2006) Nucleic Acids Res , vol.34 , pp. 3698-3707
    • Liang, S.1    Zhang, C.2    Liu, S.3    Zhou, Y.4
  • 14
    • 0036893020 scopus 로고    scopus 로고
    • Side-chain conformational entropy at protein-protein interfaces
    • 2373749, 12441384
    • Cole C, Warwicker J. Side-chain conformational entropy at protein-protein interfaces. Protein Sci 2002, 11:2860-2870. 2373749, 12441384.
    • (2002) Protein Sci , vol.11 , pp. 2860-2870
    • Cole, C.1    Warwicker, J.2
  • 15
    • 79953169868 scopus 로고    scopus 로고
    • Restricted sidechain plasticity in the structures of native proteins and complexes
    • 10.1002/pro.604, 21432939
    • Fleishman SJ, Khare SD, Koga N, Baker D. Restricted sidechain plasticity in the structures of native proteins and complexes. Protein Sci 2011, 20:753-757. 10.1002/pro.604, 21432939.
    • (2011) Protein Sci , vol.20 , pp. 753-757
    • Fleishman, S.J.1    Khare, S.D.2    Koga, N.3    Baker, D.4
  • 17
    • 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. JMolBiol 1997, 272:133.
    • (1997) JMolBiol , vol.272 , pp. 133
    • Jones, S.1    Thornton, J.M.2
  • 18
    • 0036122073 scopus 로고    scopus 로고
    • Prediction of protein--protein interaction sites in heterocomplexes with neural networks
    • 10.1046/j.1432-1033.2002.02767.x, 11874449
    • Fariselli P, Pazos F, Valencia A, Casadio R. Prediction of protein--protein interaction sites in heterocomplexes with neural networks. Eur J Biochem 2002, 269:1356-1361. 10.1046/j.1432-1033.2002.02767.x, 11874449.
    • (2002) Eur J Biochem , vol.269 , pp. 1356-1361
    • Fariselli, P.1    Pazos, F.2    Valencia, A.3    Casadio, R.4
  • 19
    • 0038356582 scopus 로고    scopus 로고
    • Predicted protein-protein interaction sites from local sequence information
    • 10.1016/S0014-5793(03)00456-3, 12782323
    • Ofran Y, Rost B. Predicted protein-protein interaction sites from local sequence information. FEBS Lett 2003, 544:236-239. 10.1016/S0014-5793(03)00456-3, 12782323.
    • (2003) FEBS Lett , vol.544 , pp. 236-239
    • Ofran, Y.1    Rost, B.2
  • 20
    • 33846200437 scopus 로고    scopus 로고
    • Prediction-based fingerprints of protein-protein interactions
    • Porollo A, Meller J. Prediction-based fingerprints of protein-protein interactions. Proteins 2007, 66:630-645.
    • (2007) Proteins , vol.66 , pp. 630-645
    • Porollo, A.1    Meller, J.2
  • 21
    • 1842526090 scopus 로고    scopus 로고
    • ProMate: a structure based prediction program to identify the location of protein-protein binding sites
    • 10.1016/j.jmb.2004.02.040, 15050833
    • 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. 10.1016/j.jmb.2004.02.040, 15050833.
    • (2004) J Mol Biol , vol.338 , pp. 181-199
    • Neuvirth, H.1    Raz, R.2    Schreiber, G.3
  • 22
    • 17444372787 scopus 로고    scopus 로고
    • Improved prediction of protein-protein binding sites using a support vector machines approach
    • 10.1093/bioinformatics/bti242, 15613384
    • Bradford JR, Westhead DR. Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 2005, 21:1487-1494. 10.1093/bioinformatics/bti242, 15613384.
    • (2005) Bioinformatics , vol.21 , pp. 1487-1494
    • Bradford, J.R.1    Westhead, D.R.2
  • 23
    • 33748779553 scopus 로고    scopus 로고
    • Insights into protein-protein interfaces using a Bayesian network prediction method
    • 10.1016/j.jmb.2006.07.028, 16919296
    • Bradford JR, Needham CJ, Bulpitt AJ, Westhead DR. Insights into protein-protein interfaces using a Bayesian network prediction method. J Mol Biol 2006, 362:365-386. 10.1016/j.jmb.2006.07.028, 16919296.
    • (2006) J Mol Biol , vol.362 , pp. 365-386
    • Bradford, J.R.1    Needham, C.J.2    Bulpitt, A.J.3    Westhead, D.R.4
  • 24
    • 33646044395 scopus 로고    scopus 로고
    • WHISCY: what information does surface conservation yield? Application to data-driven docking
    • 10.1002/prot.20842, 16450362
    • de Vries SJ, van Dijk ADJ, Bonvin AMJJ. WHISCY: what information does surface conservation yield? Application to data-driven docking. Proteins 2006, 63:479-489. 10.1002/prot.20842, 16450362.
    • (2006) Proteins , vol.63 , pp. 479-489
    • de Vries, S.J.1    van Dijk, A.D.J.2    Bonvin, A.M.J.J.3
  • 25
    • 59149087824 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites in sequences and 3D structures by random forests
    • 10.1371/journal.pcbi.1000278, 2621338, 19180183
    • Sikic M, Tomic S, Vlahovicek K. Prediction of protein-protein interaction sites in sequences and 3D structures by random forests. PLoS Comput Biol 2009, 5:e1000278. 10.1371/journal.pcbi.1000278, 2621338, 19180183.
    • (2009) PLoS Comput Biol , vol.5
    • Sikic, M.1    Tomic, S.2    Vlahovicek, K.3
  • 26
    • 0036328221 scopus 로고    scopus 로고
    • Calculations of protein volumes: sensitivity analysis and parameter database
    • 10.1093/bioinformatics/18.7.985, 12117797
    • Tsai J, Gerstein M. Calculations of protein volumes: sensitivity analysis and parameter database. Bioinformatics 2002, 18:985-995. 10.1093/bioinformatics/18.7.985, 12117797.
    • (2002) Bioinformatics , vol.18 , pp. 985-995
    • Tsai, J.1    Gerstein, M.2
  • 27
    • 33748171998 scopus 로고    scopus 로고
    • Revisiting the Voronoi description of protein-protein interfaces
    • 10.1110/ps.062245906, 2242599, 16943442
    • Cazals F, Proust F, Bahadur RP, Janin J. Revisiting the Voronoi description of protein-protein interfaces. Protein Sci 2006, 15:2082-2092. 10.1110/ps.062245906, 2242599, 16943442.
    • (2006) Protein Sci , vol.15 , pp. 2082-2092
    • Cazals, F.1    Proust, F.2    Bahadur, R.P.3    Janin, J.4
  • 28
    • 17444368331 scopus 로고    scopus 로고
    • Voro3D: 3D Voronoi tessellations applied to protein structures
    • 10.1093/bioinformatics/bth365, 15217822
    • Dupuis F, Sadoc JF, Jullien R, Angelov B, Mornon JP. Voro3D: 3D Voronoi tessellations applied to protein structures. Bioinformatics 2005, 21:1715-1716. 10.1093/bioinformatics/bth365, 15217822.
    • (2005) Bioinformatics , vol.21 , pp. 1715-1716
    • Dupuis, F.1    Sadoc, J.F.2    Jullien, R.3    Angelov, B.4    Mornon, J.P.5
  • 29
    • 0002052671 scopus 로고    scopus 로고
    • On the definition and the construction of pockets in macromolecules
    • Edelsbrunner H, Facello M, Liang J. On the definition and the construction of pockets in macromolecules. Discrete Appl Math 1998, 88:83-102.
    • (1998) Discrete Appl Math , vol.88 , pp. 83-102
    • Edelsbrunner, H.1    Facello, M.2    Liang, J.3
  • 30
    • 0032190305 scopus 로고    scopus 로고
    • Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape
    • Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S. Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins 1998, 33:1-17.
    • (1998) Proteins , vol.33 , pp. 1-17
    • Liang, J.1    Edelsbrunner, H.2    Fu, P.3    Sudhakar, P.V.4    Subramaniam, S.5
  • 31
    • 57349132441 scopus 로고    scopus 로고
    • Protein-protein docking benchmark version 3.0
    • 10.1002/prot.22106, 2726780, 18491384
    • Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. Protein-protein docking benchmark version 3.0. Proteins 2008, 73:705-709. 10.1002/prot.22106, 2726780, 18491384.
    • (2008) Proteins , vol.73 , pp. 705-709
    • Hwang, H.1    Pierce, B.2    Mintseris, J.3    Janin, J.4    Weng, Z.5
  • 33
    • 0038187615 scopus 로고    scopus 로고
    • A protein-protein docking benchmark
    • 10.1002/prot.10390, 12784372
    • Chen R, Mintseris J, Janin J, Weng Z. A protein-protein docking benchmark. Proteins 2003, 52:88-91. 10.1002/prot.10390, 12784372.
    • (2003) Proteins , vol.52 , pp. 88-91
    • Chen, R.1    Mintseris, J.2    Janin, J.3    Weng, Z.4
  • 35
    • 0037229456 scopus 로고    scopus 로고
    • Analysing six types of protein-protein interfaces
    • 10.1016/S0022-2836(02)01223-8, 12488102
    • Ofran Y, Rost B. Analysing six types of protein-protein interfaces. J Mol Biol 2003, 325:377-387. 10.1016/S0022-2836(02)01223-8, 12488102.
    • (2003) J Mol Biol , vol.325 , pp. 377-387
    • Ofran, Y.1    Rost, B.2
  • 37
    • 0345040873 scopus 로고    scopus 로고
    • Classification and Regression by randomForest
    • Liaw A, Wiener M. Classification and Regression by randomForest. R News 2002, 2:18-22.
    • (2002) R News , vol.2 , pp. 18-22
    • Liaw, A.1    Wiener, M.2
  • 38
    • 46049119818 scopus 로고    scopus 로고
    • StAR: a simple tool for the statistical comparison of ROC curves
    • 10.1186/1471-2105-9-265, 2435548, 18534022
    • Vergara IA, Norambuena T, Ferrada E, Slater AW, Melo F. StAR: a simple tool for the statistical comparison of ROC curves. BMC Bioinformatics 2008, 9:265. 10.1186/1471-2105-9-265, 2435548, 18534022.
    • (2008) BMC Bioinformatics , vol.9 , pp. 265
    • Vergara, I.A.1    Norambuena, T.2    Ferrada, E.3    Slater, A.W.4    Melo, F.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.