메뉴 건너뛰기




Volumn 12, Issue , 2011, Pages

Prediction of protein-binding areas by small-world residue networks and application to docking

Author keywords

Binding site prediction; Protein interactions; Protein protein docking; Pydock; Small world networks

Indexed keywords

BINDING SITE PREDICTIONS; EXPERIMENTAL TECHNIQUES; PROTEIN INTERACTION; PROTEIN-PROTEIN BINDING; PROTEIN-PROTEIN DOCKING; PROTEIN-PROTEIN INTERACTIONS; PYDOCK; STRUCTURAL CHARACTERIZATION;

EID: 80053341922     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-378     Document Type: Article
Times cited : (47)

References (38)
  • 2
    • 33644550021 scopus 로고    scopus 로고
    • Structural systems biology: modelling protein interactions
    • 10.1038/nrm1859, 16496021
    • Aloy P, Russell RB. Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 2006, 7:188-197. 10.1038/nrm1859, 16496021.
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 188-197
    • Aloy, P.1    Russell, R.B.2
  • 4
    • 37249065351 scopus 로고    scopus 로고
    • The molecular sociology of the cell
    • 10.1038/nature06523, 18075576
    • Robinson CV, Sali A, Baumeister W. The molecular sociology of the cell. Nature 2007, 450:973-982. 10.1038/nature06523, 18075576.
    • (2007) Nature , vol.450 , pp. 973-982
    • Robinson, C.V.1    Sali, A.2    Baumeister, W.3
  • 5
    • 48749103296 scopus 로고    scopus 로고
    • Integrating diverse data for structure determination of macromolecular assemblies
    • 10.1146/annurev.biochem.77.060407.135530, 18318657
    • Alber F, Förster F, Korkin D, Topf M, Sali A. Integrating diverse data for structure determination of macromolecular assemblies. Annu Rev Biochem 2008, 77:443-477. 10.1146/annurev.biochem.77.060407.135530, 18318657.
    • (2008) Annu Rev Biochem , vol.77 , pp. 443-477
    • Alber, F.1    Förster, F.2    Korkin, D.3    Topf, M.4    Sali, A.5
  • 6
    • 41949111630 scopus 로고    scopus 로고
    • Recent progress and future directions in protein-protein docking
    • 10.2174/138920308783565741, 18336319
    • Ritchie DW. Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci 2008, 9:1-15. 10.2174/138920308783565741, 18336319.
    • (2008) Curr Protein Pept Sci , vol.9 , pp. 1-15
    • Ritchie, D.W.1
  • 7
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • 10.1006/jmbi.1997.1203, 9299341
    • Gabb HA, Jackson RM, Sternberg MJ. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997, 272:106-120. 10.1006/jmbi.1997.1203, 9299341.
    • (1997) J Mol Biol , vol.272 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.3
  • 8
    • 33749020839 scopus 로고    scopus 로고
    • PIPER: an FFT-based protein docking program with pairwise potentials
    • 10.1002/prot.21117, 16933295
    • Kozakov D, Brenke R, Comeau SR, Vajda S. PIPER: an FFT-based protein docking program with pairwise potentials. Proteins 2006, 65:392-406. 10.1002/prot.21117, 16933295.
    • (2006) Proteins , vol.65 , pp. 392-406
    • Kozakov, D.1    Brenke, R.2    Comeau, S.R.3    Vajda, S.4
  • 9
    • 35449008122 scopus 로고    scopus 로고
    • Integrating statistical pair potentials into protein complex prediction
    • 10.1002/prot.21502, 17623839
    • Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z. Integrating statistical pair potentials into protein complex prediction. Proteins 2007, 69:511-520. 10.1002/prot.21502, 17623839.
    • (2007) Proteins , vol.69 , pp. 511-520
    • Mintseris, J.1    Pierce, B.2    Wiehe, K.3    Anderson, R.4    Chen, R.5    Weng, Z.6
  • 10
  • 11
    • 0033562633 scopus 로고    scopus 로고
    • Use of pair potentials across protein interfaces in screening predicted docked complexes
    • 10.1002/(SICI)1097-0134(19990515)35:3<364::AID-PROT11>3.0.CO;2-4, 10328272
    • Moont G, Gabb HA, Sternberg MJ. Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 1999, 35:364-373. 10.1002/(SICI)1097-0134(19990515)35:3<364::AID-PROT11>3.0.CO;2-4, 10328272.
    • (1999) Proteins , vol.35 , pp. 364-373
    • Moont, G.1    Gabb, H.A.2    Sternberg, M.J.3
  • 12
    • 21644435306 scopus 로고    scopus 로고
    • ATTRACT: protein-protein docking in CAPRI using a reduced protein model
    • 10.1002/prot.20566, 15981270
    • Zacharias M. ATTRACT: protein-protein docking in CAPRI using a reduced protein model. Proteins 2005, 60:252-256. 10.1002/prot.20566, 15981270.
    • (2005) Proteins , vol.60 , pp. 252-256
    • Zacharias, M.1
  • 13
    • 79952132540 scopus 로고    scopus 로고
    • Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein-Protein Docking
    • 10.1021/ci100353e, 21214199
    • Pons C, Talavera D, de la Cruz X, Orozco M, Fernandez-Recio J. Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein-Protein Docking. J Chem Inf Model 2011, 51:370-377. 10.1021/ci100353e, 21214199.
    • (2011) J Chem Inf Model , vol.51 , pp. 370-377
    • Pons, C.1    Talavera, D.2    de la Cruz, X.3    Orozco, M.4    Fernandez-Recio, J.5
  • 15
    • 0242720597 scopus 로고    scopus 로고
    • Uncovering network systems within protein structures
    • 10.1016/j.jmb.2003.08.061, 14636602
    • Greene LH, Higman VA. Uncovering network systems within protein structures. J Mol Biol 2003, 334:781-791. 10.1016/j.jmb.2003.08.061, 14636602.
    • (2003) J Mol Biol , vol.334 , pp. 781-791
    • Greene, L.H.1    Higman, V.A.2
  • 16
    • 0346057951 scopus 로고    scopus 로고
    • Small-world communication of residues and significance for protein dynamics
    • 10.1016/S0006-3495(04)74086-2, 1303839, 14695252
    • Atilgan AR, Akan P, Baysal C. Small-world communication of residues and significance for protein dynamics. Biophys J 2004, 86:85-91. 10.1016/S0006-3495(04)74086-2, 1303839, 14695252.
    • (2004) Biophys J , vol.86 , pp. 85-91
    • Atilgan, A.R.1    Akan, P.2    Baysal, C.3
  • 18
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of "small-world" networks
    • 10.1038/30918, 9623998
    • Watts DJ, Strogatz SH. Collective dynamics of "small-world" networks. Nature 1998, 393:440-442. 10.1038/30918, 9623998.
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 19
    • 12944331889 scopus 로고    scopus 로고
    • Small-world network approach to identify key residues in protein-protein interaction
    • del Sol A, O'Meara P. Small-world network approach to identify key residues in protein-protein interaction. Proteins 2005, 58:672-682.
    • (2005) Proteins , vol.58 , pp. 672-682
    • del Sol, A.1    O'Meara, P.2
  • 20
    • 33748207211 scopus 로고    scopus 로고
    • Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families
    • 10.1110/ps.062249106, 2242611, 16882992
    • del Sol A, Fujihashi H, Amoros D, Nussinov R. Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. Protein Sci 2006, 15:2120-2128. 10.1110/ps.062249106, 2242611, 16882992.
    • (2006) Protein Sci , vol.15 , pp. 2120-2128
    • del Sol, A.1    Fujihashi, H.2    Amoros, D.3    Nussinov, R.4
  • 21
    • 52949123643 scopus 로고    scopus 로고
    • Insights into protein-DNA interactions through structure network analysis
    • 10.1371/journal.pcbi.1000170, 2518215, 18773096
    • Sathyapriya R, Vijayabaskar MS, Vishveshwara S. Insights into protein-DNA interactions through structure network analysis. PLoS Comput Biol 2008, 4:e1000170. 10.1371/journal.pcbi.1000170, 2518215, 18773096.
    • (2008) PLoS Comput Biol , vol.4
    • Sathyapriya, R.1    Vijayabaskar, M.S.2    Vishveshwara, S.3
  • 22
    • 71749114914 scopus 로고    scopus 로고
    • Exploiting structural and topological information to improve prediction of RNA-protein binding sites
    • 10.1186/1471-2105-10-341, 2774325, 19835626
    • Maetschke SR, Yuan Z. Exploiting structural and topological information to improve prediction of RNA-protein binding sites. BMC Bioinformatics 2009, 10:341. 10.1186/1471-2105-10-341, 2774325, 19835626.
    • (2009) BMC Bioinformatics , vol.10 , pp. 341
    • Maetschke, S.R.1    Yuan, Z.2
  • 23
    • 8544221118 scopus 로고    scopus 로고
    • Network analysis of protein structures identifies functional residues
    • 10.1016/j.jmb.2004.10.055, 15544817
    • Amitai G, Shemesh A, Sitbon E, Shklar M, Netanely D, Venger I, Pietrokovski S. Network analysis of protein structures identifies functional residues. J Mol Biol 2004, 344:1135-1146. 10.1016/j.jmb.2004.10.055, 15544817.
    • (2004) J Mol Biol , vol.344 , pp. 1135-1146
    • Amitai, G.1    Shemesh, A.2    Sitbon, E.3    Shklar, M.4    Netanely, D.5    Venger, I.6    Pietrokovski, S.7
  • 24
    • 34347326305 scopus 로고    scopus 로고
    • Ligand binding and circular permutation modify residue interaction network in DHFR
    • 10.1371/journal.pcbi.0030117, 1892607, 17571919
    • Hu Z, Bowen D, Southerland WM, del Sol A, Pan Y, Nussinov R, Ma B. Ligand binding and circular permutation modify residue interaction network in DHFR. PLoS Comput Biol 2007, 3:e117. 10.1371/journal.pcbi.0030117, 1892607, 17571919.
    • (2007) PLoS Comput Biol , vol.3
    • Hu, Z.1    Bowen, D.2    Southerland, W.M.3    del Sol, A.4    Pan, Y.5    Nussinov, R.6    Ma, B.7
  • 25
    • 74549198198 scopus 로고    scopus 로고
    • Defining an essence of structure determining residue contacts in proteins
    • 10.1371/journal.pcbi.1000584, 2778133, 19997489
    • Sathyapriya R, Duarte JM, Stehr H, Filippis I, Lappe M. Defining an essence of structure determining residue contacts in proteins. PLoS Comput Biol 2009, 5:e1000584. 10.1371/journal.pcbi.1000584, 2778133, 19997489.
    • (2009) PLoS Comput Biol , vol.5
    • Sathyapriya, R.1    Duarte, J.M.2    Stehr, H.3    Filippis, I.4    Lappe, M.5
  • 26
    • 40149105312 scopus 로고    scopus 로고
    • Computer-based screening of functional conformers of proteins
    • 10.1371/journal.pcbi.1000009, 2265533, 18463705
    • Montiel Molina HM, Millán-Pacheco C, Pastor N, del Rio G. Computer-based screening of functional conformers of proteins. PLoS Comput Biol 2008, 4:e1000009. 10.1371/journal.pcbi.1000009, 2265533, 18463705.
    • (2008) PLoS Comput Biol , vol.4
    • Montiel Molina, H.M.1    Millán-Pacheco, C.2    Pastor, N.3    del Rio, G.4
  • 27
    • 70449534683 scopus 로고    scopus 로고
    • The protein meta-structure: a novel concept for chemical and molecular biology
    • 10.1007/s00018-009-0117-0, 19690801
    • Konrat R. The protein meta-structure: a novel concept for chemical and molecular biology. Cell Mol Life Sci 2009, 66:3625-3639. 10.1007/s00018-009-0117-0, 19690801.
    • (2009) Cell Mol Life Sci , vol.66 , pp. 3625-3639
    • Konrat, R.1
  • 28
    • 49249088964 scopus 로고    scopus 로고
    • Revealing unique properties of the ribosome using a network based analysis
    • 10.1093/nar/gkn433, 2504294, 18625614
    • David-Eden H, Mandel-Gutfreund Y. Revealing unique properties of the ribosome using a network based analysis. Nucleic Acids Res 2008, 36:4641-4652. 10.1093/nar/gkn433, 2504294, 18625614.
    • (2008) Nucleic Acids Res , vol.36 , pp. 4641-4652
    • David-Eden, H.1    Mandel-Gutfreund, Y.2
  • 29
    • 41449100252 scopus 로고    scopus 로고
    • Amino acid network and its scoring application in protein-protein docking
    • 10.1016/j.bpc.2007.12.005, 18329160
    • Chang S, Jiao X, Li C-H, Gong X-Q, Chen W-Z, Wang C-X. Amino acid network and its scoring application in protein-protein docking. Biophys Chem 2008, 134:111-118. 10.1016/j.bpc.2007.12.005, 18329160.
    • (2008) Biophys Chem , vol.134 , pp. 111-118
    • Chang, S.1    Jiao, X.2    Li, C.-H.3    Gong, X.-Q.4    Chen, W.-Z.5    Wang, C.-X.6
  • 30
    • 34250882254 scopus 로고    scopus 로고
    • PyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking
    • 10.1002/prot.21419, 17444519
    • Cheng TM-K, Blundell TL, Fernandez-Recio J. pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking. Proteins 2007, 68:503-515. 10.1002/prot.21419, 17444519.
    • (2007) Proteins , vol.68 , pp. 503-515
    • Cheng, T.M.-K.1    Blundell, T.L.2    Fernandez-Recio, J.3
  • 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
  • 32
    • 77957944014 scopus 로고    scopus 로고
    • Protein-protein docking benchmark version 4.0
    • 10.1002/prot.22830, 20806234
    • Hwang H, Vreven T, Janin J, Weng Z. Protein-protein docking benchmark version 4.0. Proteins 2010, 78:3111-3114. 10.1002/prot.22830, 20806234.
    • (2010) Proteins , vol.78 , pp. 3111-3114
    • Hwang, H.1    Vreven, T.2    Janin, J.3    Weng, Z.4
  • 33
    • 77949382951 scopus 로고    scopus 로고
    • Present and future challenges and limitations in protein-protein docking
    • 10.1002/prot.22564, 19731373
    • Pons C, Grosdidier S, Solernou A, Pérez-Cano L, Fernández-Recio J. Present and future challenges and limitations in protein-protein docking. Proteins 2010, 78:95-108. 10.1002/prot.22564, 19731373.
    • (2010) Proteins , vol.78 , pp. 95-108
    • Pons, C.1    Grosdidier, S.2    Solernou, A.3    Pérez-Cano, L.4    Fernández-Recio, J.5
  • 34
    • 79952685998 scopus 로고    scopus 로고
    • A geometry-based generic predictor for catalytic and allosteric sites
    • 10.1093/protein/gzq115, 21159618
    • Mitternacht S, Berezovsky IN. A geometry-based generic predictor for catalytic and allosteric sites. Protein Eng Des Sel 2011, 24:405-409. 10.1093/protein/gzq115, 21159618.
    • (2011) Protein Eng Des Sel , vol.24 , pp. 405-409
    • Mitternacht, S.1    Berezovsky, I.N.2
  • 35
    • 0037173002 scopus 로고    scopus 로고
    • Topological determinants of protein folding
    • 10.1073/pnas.122076099, 124342, 12084924
    • Dokholyan NV, Li L, Ding F, Shakhnovich EI. Topological determinants of protein folding. Proc Natl Acad Sci USA 2002, 99:8637-8641. 10.1073/pnas.122076099, 124342, 12084924.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 8637-8641
    • Dokholyan, N.V.1    Li, L.2    Ding, F.3    Shakhnovich, E.I.4
  • 37
    • 36749053938 scopus 로고    scopus 로고
    • Prediction and scoring of docking poses with pyDock
    • 10.1002/prot.21796, 17876821
    • Grosdidier S, Pons C, Solernou A, Fernández-Recio J. Prediction and scoring of docking poses with pyDock. Proteins 2007, 69:852-858. 10.1002/prot.21796, 17876821.
    • (2007) Proteins , vol.69 , pp. 852-858
    • Grosdidier, S.1    Pons, C.2    Solernou, A.3    Fernández-Recio, J.4
  • 38
    • 77957950490 scopus 로고    scopus 로고
    • Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding
    • 10.1002/prot.22773, 20602351
    • Pons C, Solernou A, Perez-Cano L, Grosdidier S, Fernandez-Recio J. Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding. Proteins 2010, 78:3182-3188. 10.1002/prot.22773, 20602351.
    • (2010) Proteins , vol.78 , pp. 3182-3188
    • Pons, C.1    Solernou, A.2    Perez-Cano, L.3    Grosdidier, S.4    Fernandez-Recio, J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.