메뉴 건너뛰기




Volumn 16, Issue 2, 2008, Pages 269-279

Funnel Hunting in a Rough Terrain: Learning and Discriminating Native Energy Funnels

Author keywords

PROTEINS

Indexed keywords

CYCLOPHILIN;

EID: 38949083887     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2007.11.013     Document Type: Article
Times cited : (28)

References (54)
  • 1
    • 1042275583 scopus 로고    scopus 로고
    • A dissection of specific and non-specific protein-protein interfaces
    • Bahadur R.P., Chakrabarti P., Rodier F., and Janin J. A dissection of specific and non-specific protein-protein interfaces. J. Mol. Biol. 336 (2004) 943-955
    • (2004) J. Mol. Biol. , vol.336 , pp. 943-955
    • Bahadur, R.P.1    Chakrabarti, P.2    Rodier, F.3    Janin, J.4
  • 2
    • 33644843079 scopus 로고    scopus 로고
    • Accounting for loop flexibility during protein-protein docking
    • Bastard K., Prevost C., and Zacharias M. Accounting for loop flexibility during protein-protein docking. Proteins 62 (2006) 956-969
    • (2006) Proteins , vol.62 , pp. 956-969
    • Bastard, K.1    Prevost, C.2    Zacharias, M.3
  • 3
    • 22444434743 scopus 로고    scopus 로고
    • Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces
    • Ben-Shimon A., and Eisenstein M. Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces. J. Mol. Biol. 351 (2005) 309-326
    • (2005) J. Mol. Biol. , vol.351 , pp. 309-326
    • Ben-Shimon, A.1    Eisenstein, M.2
  • 5
    • 34047129815 scopus 로고    scopus 로고
    • A new protein-protein docking scoring function based on interface residue properties
    • Bernauer J., Aze J., Janin J., and Poupon A. A new protein-protein docking scoring function based on interface residue properties. Bioinformatics 23 (2007) 555-562
    • (2007) Bioinformatics , vol.23 , pp. 555-562
    • Bernauer, J.1    Aze, J.2    Janin, J.3    Poupon, A.4
  • 6
    • 33645961330 scopus 로고    scopus 로고
    • Flexible protein-protein docking
    • Bonvin A.M. Flexible protein-protein docking. Curr. Opin. Struct. Biol. 16 (2006) 194-200
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 194-200
    • Bonvin, A.M.1
  • 7
    • 23044487169 scopus 로고    scopus 로고
    • Statistical analysis and prediction of protein-protein interfaces
    • Bordner A.J., and Abagyan R. Statistical analysis and prediction of protein-protein interfaces. Proteins 60 (2005) 353-366
    • (2005) Proteins , vol.60 , pp. 353-366
    • Bordner, A.J.1    Abagyan, R.2
  • 8
    • 0346733329 scopus 로고    scopus 로고
    • Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
    • Caffrey D.R., Somaroo S., Hughes J.D., Mintseris J., and Huang E.S. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?. Protein Sci. 13 (2004) 190-202
    • (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
  • 9
    • 0032981961 scopus 로고    scopus 로고
    • Free energy landscapes of encounter complexes in protein-protein association
    • Camacho C.J., Weng Z., Vajda S., and DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophys. J. 76 (1999) 1166-1178
    • (1999) Biophys. J. , vol.76 , pp. 1166-1178
    • Camacho, C.J.1    Weng, Z.2    Vajda, S.3    DeLisi, C.4
  • 10
    • 33645095436 scopus 로고    scopus 로고
    • Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment
    • Chelliah V., Blundell T.L., and Fernandez-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 (2006) 1669-1682
    • (2006) J. Mol. Biol. , vol.357 , pp. 1669-1682
    • Chelliah, V.1    Blundell, T.L.2    Fernandez-Recio, J.3
  • 11
  • 12
    • 34249753618 scopus 로고
    • Support vector networks
    • Cortes C., and Vapnik V. Support vector networks. Mach. Learn. 20 (1995) 273-293
    • (1995) Mach. Learn. , vol.20 , pp. 273-293
    • Cortes, C.1    Vapnik, V.2
  • 13
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill K.A., and Chan H.S. From Levinthal to pathways to funnels. Nat. Struct. Biol. 4 (1997) 10-19
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 14
    • 0036228167 scopus 로고    scopus 로고
    • Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics
    • Dima R.I., and Thirumalai D. Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics. Protein Sci. 11 (2002) 1036-1049
    • (2002) Protein Sci. , vol.11 , pp. 1036-1049
    • Dima, R.I.1    Thirumalai, D.2
  • 15
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: a protein-protein docking approach based on biochemical or biophysical information
    • Dominguez C., Boelens R., and Bonvin A.M. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125 (2003) 1731-1737
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.3
  • 16
    • 17344380633 scopus 로고    scopus 로고
    • ICM-Dros. Inf. Serv.CO docking by global energy optimization with fully flexible side-chains
    • Fernandez-Recio J., Totrov M., and Abagyan R. ICM-Dros. Inf. Serv.CO docking by global energy optimization with fully flexible side-chains. Proteins 52 (2003) 113-117
    • (2003) Proteins , vol.52 , pp. 113-117
    • Fernandez-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 18
    • 12944257228 scopus 로고    scopus 로고
    • The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures
    • Glaser F., Rosenberg Y., Kessel A., Pupko T., and Ben-Tal N. The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures. Proteins 58 (2005) 610-617
    • (2005) Proteins , vol.58 , pp. 610-617
    • Glaser, F.1    Rosenberg, Y.2    Kessel, A.3    Pupko, T.4    Ben-Tal, N.5
  • 19
    • 33646472024 scopus 로고    scopus 로고
    • High-resolution protein-protein docking
    • Gray J.J. High-resolution protein-protein docking. Curr. Opin. Struct. Biol. 16 (2006) 183-193
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 183-193
    • Gray, J.J.1
  • 20
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray J.J., Moughon S., Wang C., Schueler-Furman O., Kuhlman B., Rohl C.A., and Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol. 331 (2003) 281-299
    • (2003) J. Mol. Biol. , vol.331 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7
  • 21
    • 0036161259 scopus 로고    scopus 로고
    • Gene selection for cancer classification using support vector machines
    • Guyon I., Weston J., Barnhill S., and Vapnik V. Gene selection for cancer classification using support vector machines. Mach. Learn. 46 (2002) 389-422
    • (2002) Mach. Learn. , vol.46 , pp. 389-422
    • Guyon, I.1    Weston, J.2    Barnhill, S.3    Vapnik, V.4
  • 22
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: an overview of search algorithms and a guide to scoring functions
    • Halperin I., Ma B., Wolfson H., and Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 47 (2002) 409-443
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 23
    • 13244262600 scopus 로고    scopus 로고
    • Assessing predictions of protein-protein interaction: the CAPRI experiment
    • Janin J. Assessing predictions of protein-protein interaction: the CAPRI experiment. Protein Sci. 14 (2005) 278-283
    • (2005) Protein Sci. , vol.14 , pp. 278-283
    • Janin, J.1
  • 24
    • 0002714543 scopus 로고    scopus 로고
    • Making large-scale SVM learning practical
    • Schoelkopf C., Burges C., and Smola A. (Eds), MIT Press, Cambridge, MA
    • Joachims T. Making large-scale SVM learning practical. In: Schoelkopf C., Burges C., and Smola A. (Eds). Advances in Kernel Methods-Support Vector Learning (1999), MIT Press, Cambridge, MA
    • (1999) Advances in Kernel Methods-Support Vector Learning
    • Joachims, T.1
  • 25
    • 38949116518 scopus 로고    scopus 로고
    • Kohavi, R. (1995). A study of crossvalidation and bootstrap for accuracy estimation and model selection. Paper presented at Proceedings of the Fourteenth International Joint Conference on Artificial Intelligence (San Mateo, CA).
    • Kohavi, R. (1995). A study of crossvalidation and bootstrap for accuracy estimation and model selection. Paper presented at Proceedings of the Fourteenth International Joint Conference on Artificial Intelligence (San Mateo, CA).
  • 26
    • 38949197309 scopus 로고    scopus 로고
    • Discrimination of near-native structures in protein-protein docking by testing the stability of local minima
    • in press
    • Kosakov D., Schueler-Furman O., and Vajda S. Discrimination of near-native structures in protein-protein docking by testing the stability of local minima. Proteins (2007) in press
    • (2007) Proteins
    • Kosakov, D.1    Schueler-Furman, O.2    Vajda, S.3
  • 27
    • 13444301037 scopus 로고    scopus 로고
    • A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes
    • Levy Y., Cho S.S., Onuchic J.N., and Wolynes P.G. A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. J. Mol. Biol. 346 (2005) 1121-1145
    • (2005) J. Mol. Biol. , vol.346 , pp. 1121-1145
    • Levy, Y.1    Cho, S.S.2    Onuchic, J.N.3    Wolynes, P.G.4
  • 28
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multiple-minima problem in protein folding
    • Li Z., and Scheraga H.A. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc. Natl. Acad. Sci. USA 84 (1987) 6611-6615
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 29
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo Conte L., Chothia C., and Janin J. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285 (1999) 2177-2198
    • (1999) J. Mol. Biol. , vol.285 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 30
    • 36749091035 scopus 로고    scopus 로고
    • Assessing the energy landscape of CAPRI Targets by FunHunt
    • London N., and Schueler-Furman O. Assessing the energy landscape of CAPRI Targets by FunHunt. Proteins 69 (2007) 809-815
    • (2007) Proteins , vol.69 , pp. 809-815
    • London, N.1    Schueler-Furman, O.2
  • 31
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald I.K., and Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238 (1994) 777-793
    • (1994) J. Mol. Biol. , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 32
    • 1842526090 scopus 로고    scopus 로고
    • ProMate: a structure based prediction program to identify the location of protein-protein binding sites
    • Neuvirth H., Raz R., and Schreiber G. ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J. Mol. Biol. 338 (2004) 181-199
    • (2004) J. Mol. Biol. , vol.338 , pp. 181-199
    • Neuvirth, H.1    Raz, R.2    Schreiber, G.3
  • 34
    • 34248579768 scopus 로고    scopus 로고
    • A simple shape characteristic of protein-protein recognition
    • Nicola G., and Vakser I.A. A simple shape characteristic of protein-protein recognition. Bioinformatics 23 (2007) 789-792
    • (2007) Bioinformatics , vol.23 , pp. 789-792
    • Nicola, G.1    Vakser, I.A.2
  • 35
    • 0037474541 scopus 로고    scopus 로고
    • Structural characterisation and functional significance of transient protein-protein interactions
    • Nooren I.M., and Thornton J.M. Structural characterisation and functional significance of transient protein-protein interactions. J. Mol. Biol. 325 (2003) 991-1018
    • (2003) J. Mol. Biol. , vol.325 , pp. 991-1018
    • Nooren, I.M.1    Thornton, J.M.2
  • 38
    • 34248513078 scopus 로고    scopus 로고
    • ZRANK: reranking protein docking predictions with an optimized energy function
    • Pierce B., and Weng Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 67 (2007) 1078-1086
    • (2007) Proteins , vol.67 , pp. 1078-1086
    • Pierce, B.1    Weng, Z.2
  • 42
    • 0037153276 scopus 로고    scopus 로고
    • A general expression for bimolecular association rates with orientational constraints
    • Schlosshauer M., and Baker D. A general expression for bimolecular association rates with orientational constraints. J. Phys. Chem. B 106 (2002) 12079-12083
    • (2002) J. Phys. Chem. B , vol.106 , pp. 12079-12083
    • Schlosshauer, M.1    Baker, D.2
  • 43
    • 2442640122 scopus 로고    scopus 로고
    • Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness
    • Schlosshauer M., and Baker D. Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein Sci. 13 (2004) 1660-1669
    • (2004) Protein Sci. , vol.13 , pp. 1660-1669
    • Schlosshauer, M.1    Baker, D.2
  • 45
    • 21644459373 scopus 로고    scopus 로고
    • Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility
    • Schueler-Furman O., Wang C., and Baker D. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins 60 (2005) 187-194
    • (2005) Proteins , vol.60 , pp. 187-194
    • Schueler-Furman, O.1    Wang, C.2    Baker, D.3
  • 46
    • 27344449197 scopus 로고    scopus 로고
    • Progress in modeling of protein structures and interactions
    • Schueler-Furman O., Wang C., Bradley P., Misura K., and Baker D. Progress in modeling of protein structures and interactions. Science 310 (2005) 638-642
    • (2005) Science , vol.310 , pp. 638-642
    • Schueler-Furman, O.1    Wang, C.2    Bradley, P.3    Misura, K.4    Baker, D.5
  • 47
    • 0032530578 scopus 로고    scopus 로고
    • Clustering of low-energy conformations near the native structures of small proteins
    • Shortle D., Simons K.T., and Baker D. Clustering of low-energy conformations near the native structures of small proteins. Proc. Natl. Acad. Sci. USA 95 (1998) 11158-11162
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 11158-11162
    • Shortle, D.1    Simons, K.T.2    Baker, D.3
  • 49
    • 15244355250 scopus 로고    scopus 로고
    • The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking
    • Smith G.R., Sternberg M.J., and Bates P.A. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J. Mol. Biol. 347 (2005) 1077-1101
    • (2005) J. Mol. Biol. , vol.347 , pp. 1077-1101
    • Smith, G.R.1    Sternberg, M.J.2    Bates, P.A.3
  • 50
    • 0023890867 scopus 로고
    • Measuring the accuracy of diagnostic systems
    • Swets J.A. Measuring the accuracy of diagnostic systems. Science 240 (1988) 1285-1293
    • (1988) Science , vol.240 , pp. 1285-1293
    • Swets, J.A.1
  • 51
    • 0033056708 scopus 로고    scopus 로고
    • Folding funnels, binding funnels, and protein function
    • Tsai C.J., Kumar S., Ma B., and Nussinov R. Folding funnels, binding funnels, and protein function. Protein Sci. 8 (1999) 1181-1190
    • (1999) Protein Sci. , vol.8 , pp. 1181-1190
    • Tsai, C.J.1    Kumar, S.2    Ma, B.3    Nussinov, R.4
  • 52
    • 17744364070 scopus 로고    scopus 로고
    • Improved side-chain modeling for protein-protein docking
    • Wang C., Schueler-Furman O., and Baker D. Improved side-chain modeling for protein-protein docking. Protein Sci. 14 (2005) 1328-1339
    • (2005) Protein Sci. , vol.14 , pp. 1328-1339
    • Wang, C.1    Schueler-Furman, O.2    Baker, D.3
  • 53
    • 34548861782 scopus 로고    scopus 로고
    • Incorporating backbone flexibility into protein-protein docking
    • Wang C., Bradley P., and Baker D. Incorporating backbone flexibility into protein-protein docking. J. Mol. Biol. 373 (2007) 503-519
    • (2007) J. Mol. Biol. , vol.373 , pp. 503-519
    • Wang, C.1    Bradley, P.2    Baker, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.