메뉴 건너뛰기




Volumn 49, Issue 3, 2009, Pages 693-703

Improving the accuracy of an affinity prediction method by using statistics on shape complementarity between proteins

Author keywords

[No Author keywords available]

Indexed keywords

FORECASTING;

EID: 65249135571     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci800310f     Document Type: Article
Times cited : (14)

References (44)
  • 2
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo Conte, L.; Chothia, C.; Janin, J. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 1999, 285, 2177-2198.
    • (1999) J. Mol. Biol , vol.285 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 3
    • 0033566576 scopus 로고    scopus 로고
    • Examination of shape complementarity in docking of unbound proteins
    • Norel, R.; Petrey, D.; Wolfson, H. J.; Nussinov, R. Examination of shape complementarity in docking of unbound proteins. Proteins 1999, 36, 307-317.
    • (1999) Proteins , vol.36 , pp. 307-317
    • Norel, R.1    Petrey, D.2    Wolfson, H.J.3    Nussinov, R.4
  • 4
    • 0024406857 scopus 로고
    • A novel genetic system to detect protein-protein interactions
    • Fields, S.; Song, O. A novel genetic system to detect protein-protein interactions. Nature 1989, 340, 245-246.
    • (1989) Nature , vol.340 , pp. 245-246
    • Fields, S.1    Song, O.2
  • 5
    • 0033974688 scopus 로고    scopus 로고
    • Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins
    • Ito, T.; Tashiro, K.; Muta, S.; Ozawa, R.; Chiba, T.; Nishizawa, M.; Yamamoto, K.; Kuhara, S.; Sakaki, Y. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 1143-1147.
    • (2000) Proc. Natl. Acad. Sci. U.S.A , vol.97 , pp. 1143-1147
    • Ito, T.1    Tashiro, K.2    Muta, S.3    Ozawa, R.4    Chiba, T.5    Nishizawa, M.6    Yamamoto, K.7    Kuhara, S.8    Sakaki, Y.9
  • 10
    • 0035224503 scopus 로고    scopus 로고
    • Protein-protein interaction map inference using interacting domain profile pairs
    • Wojcik, J.; Schachter, V. Protein-protein interaction map inference using interacting domain profile pairs. Bioinformatics 2001, 17, S296-S305.
    • (2001) Bioinformatics , vol.17
    • Wojcik, J.1    Schachter, V.2
  • 11
    • 0345600247 scopus 로고    scopus 로고
    • Giot, L.; Bader, J. S.; Brouwer, C.; Chaudhuri, A.; Kuang, B.; Li, Y.; Hao, Y. L.; Ooi, C. E.; Godwin, B.; Vitols, E.; Vijayadamodar, G.; Pochart, P.; Machined, H.; Welsh, M.; Kong, Y.; Zerhusen, B.; Malcolm, R.; Varrone, Z.; Collis, A.; Minto, M.; Burgess, S.; McDaniel, L.; Stimpson, E.; Spriggs, F.; Williams, J.; Neurath, K.; Ioime, N.; Agee, M.; Voss, E.; Furtak, K.; Renzulli, R.; Aanensen, N.; Carrolla, S.; Bickelhaupt, E.; Lazovatsky, Y.; DaSilva, A.; Zhong, J.; Stanyon, C. A.; Finley, R. L., Jr.; White, K. P.; Braverman, M.; Jarvie, T.; Gold, S.; Leach, M.; Knight, J.; Shimkets, R. A.; McKenna, M. P.; Chant, J.; Rothberg, J. M. A protein interaction map of Drosophila melanogaster. Science 2003, 302, 1727-1736.
    • Giot, L.; Bader, J. S.; Brouwer, C.; Chaudhuri, A.; Kuang, B.; Li, Y.; Hao, Y. L.; Ooi, C. E.; Godwin, B.; Vitols, E.; Vijayadamodar, G.; Pochart, P.; Machined, H.; Welsh, M.; Kong, Y.; Zerhusen, B.; Malcolm, R.; Varrone, Z.; Collis, A.; Minto, M.; Burgess, S.; McDaniel, L.; Stimpson, E.; Spriggs, F.; Williams, J.; Neurath, K.; Ioime, N.; Agee, M.; Voss, E.; Furtak, K.; Renzulli, R.; Aanensen, N.; Carrolla, S.; Bickelhaupt, E.; Lazovatsky, Y.; DaSilva, A.; Zhong, J.; Stanyon, C. A.; Finley, R. L., Jr.; White, K. P.; Braverman, M.; Jarvie, T.; Gold, S.; Leach, M.; Knight, J.; Shimkets, R. A.; McKenna, M. P.; Chant, J.; Rothberg, J. M. A protein interaction map of Drosophila melanogaster. Science 2003, 302, 1727-1736.
  • 12
    • 27144530248 scopus 로고    scopus 로고
    • Rual, J. F.; Venkatesan, K.; Hao, T.; Hirozane-Kishikawa, T.; Dricot, A.; Li, N.; Berriz, G. F.; Gibbons, F. D.; Dreze, M.; Ayivi-Guedehoussou, N.; Klitgord, N.; Simon, C.; Boxem, M.; Milstein, S.; Rosenberg, J.; Goldberg, D. S.; Zhang, L. V.; Wong, S. L.; Franklin, G.; Li, S.; Albala, J. S.; Lim, J.; Fraughton, C.; Llamosas, E.; Cevik, S.; Bex, C.; Lamesch, P.; Sikorski, R. S.; Vandenhaute, J.; Zoghbi, H. Y.; Smolyar, A.; Bosak, S.; Sequerra, R.; Doucette-Stamm, L.; Cusick, M. E.; Hill, D. E.; Roth, F. P.; Vidal, M. Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437, 1173-1178.
    • Rual, J. F.; Venkatesan, K.; Hao, T.; Hirozane-Kishikawa, T.; Dricot, A.; Li, N.; Berriz, G. F.; Gibbons, F. D.; Dreze, M.; Ayivi-Guedehoussou, N.; Klitgord, N.; Simon, C.; Boxem, M.; Milstein, S.; Rosenberg, J.; Goldberg, D. S.; Zhang, L. V.; Wong, S. L.; Franklin, G.; Li, S.; Albala, J. S.; Lim, J.; Fraughton, C.; Llamosas, E.; Cevik, S.; Bex, C.; Lamesch, P.; Sikorski, R. S.; Vandenhaute, J.; Zoghbi, H. Y.; Smolyar, A.; Bosak, S.; Sequerra, R.; Doucette-Stamm, L.; Cusick, M. E.; Hill, D. E.; Roth, F. P.; Vidal, M. Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437, 1173-1178.
  • 14
    • 0036568319 scopus 로고    scopus 로고
    • In silico two-hybrid system for the selection of physically interacting protein pairs
    • Pazos, F.; Valencia, A. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 2002, 47, 219-227.
    • (2002) Proteins , vol.47 , pp. 219-227
    • Pazos, F.1    Valencia, A.2
  • 15
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering, C.; Krause, R.; Snel, B.; Cornell, M.; Oliver, S. G.; Fields, S.; Bork, P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417, 399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 16
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • Smith, G. R.; Sternberg, M. J. Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol. 2002, 12, 28-35.
    • (2002) Curr. Opin. Struct. Biol , vol.12 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.2
  • 17
    • 84956979675 scopus 로고    scopus 로고
    • Efficient Unbound Docking of Rigid Molecules In, Springer-Verlag: Berlin, Heidelberg
    • Duhovny, D.; Nussinov, R.; Wolfson, H. Efficient Unbound Docking of Rigid Molecules In Algorithms in Bioinformatics; Springer-Verlag: Berlin, Heidelberg, 2002; Vol. 2452, pp 185-200.
    • (2002) Algorithms in Bioinformatics , vol.2452 , pp. 185-200
    • Duhovny, D.1    Nussinov, R.2    Wolfson, H.3
  • 18
    • 0038697840 scopus 로고    scopus 로고
    • GAPDOCK: A Genetic Algorithm Approach to Protein Docking in CAPRI round 1
    • Gardiner, E. J.; Willett, P.; Artymiuk, P. J. GAPDOCK: a Genetic Algorithm Approach to Protein Docking in CAPRI round 1. Proteins 2003, 52, 10-14.
    • (2003) Proteins , vol.52 , pp. 10-14
    • Gardiner, E.J.1    Willett, P.2    Artymiuk, P.J.3
  • 19
    • 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.; Baker, D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol. 2003, 331, 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
  • 20
    • 0034769223 scopus 로고    scopus 로고
    • Electrostatic contributions to protein-protein interactions: Fast energetic filters for docking and their physical basis
    • Norel, R.; Sheinerman, F.; Petrey, D.; Honig, B. Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis. Protein Sci. 2001, 10, 2147-2161.
    • (2001) Protein Sci , vol.10 , pp. 2147-2161
    • Norel, R.1    Sheinerman, F.2    Petrey, D.3    Honig, B.4
  • 21
    • 0034212826 scopus 로고    scopus 로고
    • Palma, P. N.; Krippahl, L.; Wampler, J. E.; Moura, J. J. Bigger: a new (soft) docking algorithm for predicting protein interactions. Proteins 2000, 39, 372-384.
    • Palma, P. N.; Krippahl, L.; Wampler, J. E.; Moura, J. J. Bigger: a new (soft) docking algorithm for predicting protein interactions. Proteins 2000, 39, 372-384.
  • 22
    • 0034332970 scopus 로고    scopus 로고
    • DARWIN: A program for docking flexible molecules
    • Taylor, J. S.; Burnett, R. M. DARWIN: a program for docking flexible molecules. Proteins 2000, 41, 173-191.
    • (2000) Proteins , vol.41 , pp. 173-191
    • Taylor, J.S.1    Burnett, R.M.2
  • 23
    • 58149467654 scopus 로고    scopus 로고
    • Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins
    • Tsukamoto, K.; Yoshikawa, T.; Hourai, Y.; Fukui, K.; Akiyama, Y. Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins. J. Bioinf. Comput. Biol 2008, 6, 1133-1156.
    • (2008) J. Bioinf. Comput. Biol , vol.6 , pp. 1133-1156
    • Tsukamoto, K.1    Yoshikawa, T.2    Hourai, Y.3    Fukui, K.4    Akiyama, Y.5
  • 24
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee, B.; Richards, F. M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 1971, 55, 379-400.
    • (1971) J. Mol. Biol , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 25
    • 38149012931 scopus 로고    scopus 로고
    • High Performance 3D Convolution for Protein Docking on IBM Blue Gene In, Springer-Verlag: Berlin, Heidelberg
    • Nukada, A.; Hourai, Y.; Nishida, A.; Akiyama, Y. High Performance 3D Convolution for Protein Docking on IBM Blue Gene In Parallel and Distributed Processing and Applications; Springer-Verlag: Berlin, Heidelberg, 2007; Vol. 4742, pp 958-969.
    • (2007) Parallel and Distributed Processing and Applications , vol.4742 , pp. 958-969
    • Nukada, A.1    Hourai, Y.2    Nishida, A.3    Akiyama, Y.4
  • 26
    • 33645970683 scopus 로고    scopus 로고
    • Relating FFTW and Split-Radix In, Springer-Verlag: Berlin, Heidelberg
    • Kiselyov, O.; Taha, W. Relating FFTW and Split-Radix In Embedded Software and Systems; Springer-Verlag: Berlin, Heidelberg, 2005; Vol. 3605, pp 488-493.
    • (2005) Embedded Software and Systems , vol.3605 , pp. 488-493
    • Kiselyov, O.1    Taha, W.2
  • 27
    • 65249097463 scopus 로고    scopus 로고
    • Code Generators for Automatic Tuning of Numerical Kernels: Experiences with FFTW Position Paper
    • Springer-Verlag: Berlin, Heidelberg
    • Vuduc, R.; Demmel, J. Code Generators for Automatic Tuning of Numerical Kernels: Experiences with FFTW Position Paper. In Semantics, Applications, and Implementation of Program Generation; Springer-Verlag: Berlin, Heidelberg, 2000; Vol. 1924, pp 190-211.
    • (2000) Semantics, Applications, and Implementation of Program Generation , vol.1924 , pp. 190-211
    • Vuduc, R.1    Demmel, J.2
  • 30
    • 35449008122 scopus 로고    scopus 로고
    • Integrating statistical pair potentials into protein complex prediction
    • 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.
    • (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
  • 31
    • 65249099241 scopus 로고    scopus 로고
    • Pierce, B.; Hourai, Y.; Weng, Z. ZDOCK 2.3.1 and ZDOCK 3.0.1: Using a New 3D Convolution Library to Enhance Docking Efficiency. Bioinformatics 2007, submitted for publication.
    • Pierce, B.; Hourai, Y.; Weng, Z. ZDOCK 2.3.1 and ZDOCK 3.0.1: Using a New 3D Convolution Library to Enhance Docking Efficiency. Bioinformatics 2007, submitted for publication.
  • 32
    • 34248513078 scopus 로고    scopus 로고
    • ZRANK: Reranking protein docking predictions with an optimized energy function
    • Pierce, B.; Weng, Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 2007, 67, 1078-1086.
    • (2007) Proteins , vol.67 , pp. 1078-1086
    • Pierce, B.1    Weng, Z.2
  • 33
    • 0038187615 scopus 로고    scopus 로고
    • A protein-protein docking benchmark
    • Chen, R.; Mintseris, J.; Janin, J.; Weng, Z. A protein-protein docking benchmark. Proteins 2003, 52, 88-91.
    • (2003) Proteins , vol.52 , pp. 88-91
    • Chen, R.1    Mintseris, J.2    Janin, J.3    Weng, Z.4
  • 36
    • 35748932852 scopus 로고    scopus 로고
    • R Development Core Team, R Foundation for Statistical Computing: Vienna, Austria
    • R Development Core Team. R: A language and environment for statistical computing; R Foundation for Statistical Computing: Vienna, Austria, 2007.
    • (2007) R: A language and environment for statistical computing
  • 37
    • 0025737887 scopus 로고
    • Three-dimensional structure of the complexes between bovine chymotrypsi-nogen A and two recombinant variants of human pancreatic secretory trypsin inhibitor (Kazal-type)
    • Hecht, H. J.; Szardenings, M.; Collins, J.; Schomburg, D. Three-dimensional structure of the complexes between bovine chymotrypsi-nogen A and two recombinant variants of human pancreatic secretory trypsin inhibitor (Kazal-type). J. Mol. Biol. 1991, 220, 711-722.
    • (1991) J. Mol. Biol , vol.220 , pp. 711-722
    • Hecht, H.J.1    Szardenings, M.2    Collins, J.3    Schomburg, D.4
  • 38
    • 0024959382 scopus 로고
    • The refined 2.0 A X-ray crystal structure of the complex formed between bovine beta-trypsin and CMTI-I, a trypsin inhibitor from squash seeds (Cucurbita maxima). Topological similarity of the squash seed inhibitors with the carboxypeptidase A inhibitor from potatoes
    • Bode, W.; Greyling, H. J.; Huber, R.; Otlewski, J.; Wilusz, T. The refined 2.0 A X-ray crystal structure of the complex formed between bovine beta-trypsin and CMTI-I, a trypsin inhibitor from squash seeds (Cucurbita maxima). Topological similarity of the squash seed inhibitors with the carboxypeptidase A inhibitor from potatoes. FEBS Lett. 1989, 242, 285-292.
    • (1989) FEBS Lett , vol.242 , pp. 285-292
    • Bode, W.1    Greyling, H.J.2    Huber, R.3    Otlewski, J.4    Wilusz, T.5
  • 39
    • 0021930156 scopus 로고
    • Bovine chymotrypsinogen A X-ray crystal structure analysis and refinement of a new crystal form at 1.8 A resolution
    • Wang, D.; Bode, W.; Huber, R. Bovine chymotrypsinogen A X-ray crystal structure analysis and refinement of a new crystal form at 1.8 A resolution. J. Mol. Biol. 1985, 185, 595-624.
    • (1985) J. Mol. Biol , vol.185 , pp. 595-624
    • Wang, D.1    Bode, W.2    Huber, R.3
  • 40
    • 0026684255 scopus 로고
    • Three-dimensional structure of a recombinant variant of human pancreatic secretory trypsin inhibitor (Kazal type)
    • Hecht, H. J.; Szardenings, M.; Collins, J.; Schomburg, D. Three-dimensional structure of a recombinant variant of human pancreatic secretory trypsin inhibitor (Kazal type). J. Mol. Biol. 1992, 225, 1095-1103.
    • (1992) J. Mol. Biol , vol.225 , pp. 1095-1103
    • Hecht, H.J.1    Szardenings, M.2    Collins, J.3    Schomburg, D.4
  • 41
    • 0028840813 scopus 로고
    • Unique binding of a novel synthetic inhibitor, N-[3-[4-[4-(amidinophenoxy)carbonyl]phenyl]-2-methyl-2-propenoyl]-N- allylglycine methanesulfonate, to bovine trypsin, revealed by the crystal structure of the complex
    • Odagaki, Y.; Nakai, H.; Senokuchi, K.; Kawamura, M.; Hamanaka, N.; Nakamura, M.; Tomoo, K.; Ishida, T. Unique binding of a novel synthetic inhibitor, N-[3-[4-[4-(amidinophenoxy)carbonyl]phenyl]-2-methyl-2-propenoyl]-N- allylglycine methanesulfonate, to bovine trypsin, revealed by the crystal structure of the complex. Biochemistry (Moscow) 1995, 34, 12849-12853.
    • (1995) Biochemistry (Moscow) , vol.34 , pp. 12849-12853
    • Odagaki, Y.1    Nakai, H.2    Senokuchi, K.3    Kawamura, M.4    Hamanaka, N.5    Nakamura, M.6    Tomoo, K.7    Ishida, T.8
  • 42
    • 0016654728 scopus 로고
    • Effect of whole-body x-irradiation on the composition and metabolism of rat brain lipids
    • Taranova, N. P. Effect of whole-body x-irradiation on the composition and metabolism of rat brain lipids. Radiobiologiia 1975, 15, 821-825.
    • (1975) Radiobiologiia , vol.15 , pp. 821-825
    • Taranova, N.P.1
  • 43
    • 21644469377 scopus 로고    scopus 로고
    • Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
    • Mendez, R.; Leplae, R.; Lensink, M. F.; Wodak, S. J. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005, 60, 150-169.
    • (2005) Proteins , vol.60 , pp. 150-169
    • Mendez, R.1    Leplae, R.2    Lensink, M.F.3    Wodak, S.J.4
  • 44
    • 51349091797 scopus 로고    scopus 로고
    • Identification of protein interaction partners and protein-protein interaction sites
    • Sacquin-Mora, S.; Carbone, A.; Lavery, R. Identification of protein interaction partners and protein-protein interaction sites. J. Mol. Biol. 2008, 382, 1276-1289.
    • (2008) J. Mol. Biol , vol.382 , pp. 1276-1289
    • Sacquin-Mora, S.1    Carbone, A.2    Lavery, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.