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Volumn 81, Issue 11, 2013, Pages 1874-1884

Sampling and scoring: A marriage made in heaven

Author keywords

CAPRI docking experiment; Conformational search; Molecular interaction; Molecular mechanics; Monte Carlo method; Protein protein docking; Scoring function; Structure refinement; Structure based potential

Indexed keywords

ALGORITHM; CRYSTAL STRUCTURE; MOLECULAR DOCKING; MONTE CARLO METHOD; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW; SAMPLING; SCORING SYSTEM;

EID: 84885074179     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24343     Document Type: Review
Times cited : (56)

References (61)
  • 1
    • 41949111630 scopus 로고    scopus 로고
    • Recent progress and future directions in protein-protein docking
    • Ritchie DW. Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci 2008;9:1-15.
    • (2008) Curr Protein Pept Sci , vol.9 , pp. 1-15
    • Ritchie, D.W.1
  • 3
    • 64549106038 scopus 로고    scopus 로고
    • Convergence and combination of methods in protein-protein docking
    • Vajda S, Kozakov D. Convergence and combination of methods in protein-protein docking. Curr Opin Struct Biol 2009;19:164-170.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 164-170
    • Vajda, S.1    Kozakov, D.2
  • 4
    • 78149450921 scopus 로고    scopus 로고
    • SKATE: a docking program that decouples systematic sampling from scoring
    • Feng JA, Marshall GR. SKATE: a docking program that decouples systematic sampling from scoring. J Comput Chem 2010;31:2540-2554.
    • (2010) J Comput Chem , vol.31 , pp. 2540-2554
    • Feng, J.A.1    Marshall, G.R.2
  • 6
    • 77957934896 scopus 로고    scopus 로고
    • Docking and scoring protein interactions: CAPRI 2009
    • Lensink MF, Wodak SJ. Docking and scoring protein interactions: CAPRI 2009. Proteins 2010;78:3073-3084.
    • (2010) Proteins , vol.78 , pp. 3073-3084
    • Lensink, M.F.1    Wodak, S.J.2
  • 7
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near native folds from well-constructed decoys
    • Park B, Levitt M. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol 1996;258:367-392.
    • (1996) J Mol Biol , vol.258 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 8
    • 0033853177 scopus 로고    scopus 로고
    • Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction
    • Samudrala R, Levitt M. Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 2000;9:1399-1401.
    • (2000) Protein Sci , vol.9 , pp. 1399-1401
    • Samudrala, R.1    Levitt, M.2
  • 9
    • 0036681394 scopus 로고    scopus 로고
    • Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model
    • Felts AK, Gallicchio E, Wallqvist A, Levy RM. Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model. Proteins 2002;48:404-422.
    • (2002) Proteins , vol.48 , pp. 404-422
    • Felts, A.K.1    Gallicchio, E.2    Wallqvist, A.3    Levy, R.M.4
  • 10
    • 0037439987 scopus 로고    scopus 로고
    • MOPED: method for optimizing physical energy parameters using decoys
    • Seok C, Rosen JB, Chodera JD, Dill KA. MOPED: method for optimizing physical energy parameters using decoys. J Comput Chem 2003;24:89-97.
    • (2003) J Comput Chem , vol.24 , pp. 89-97
    • Seok, C.1    Rosen, J.B.2    Chodera, J.D.3    Dill, K.A.4
  • 13
    • 0038008976 scopus 로고    scopus 로고
    • An improved protein decoy set for testing energy functions for protein structure prediction
    • Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D. An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 2003;53:76-87.
    • (2003) Proteins , vol.53 , pp. 76-87
    • Tsai, J.1    Bonneau, R.2    Morozov, A.V.3    Kuhlman, B.4    Rohl, C.A.5    Baker, D.6
  • 14
    • 0141978673 scopus 로고    scopus 로고
    • Comparative protein structure modeling by iterative alignment, model building and model assessment
    • John B, Sali A. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res 2003;31:3982-3992.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3982-3992
    • John, B.1    Sali, A.2
  • 15
    • 78149453870 scopus 로고    scopus 로고
    • A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction
    • Zhang J, Zhang Y. A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction. PLoS One 2010;5:e15386.
    • (2010) PLoS One , vol.5
    • Zhang, J.1    Zhang, Y.2
  • 17
    • 0025785057 scopus 로고
    • Protein docking and complementarity
    • Shoichet BK, Kuntz ID. Protein docking and complementarity. J Mol Biol 1991;221:327-346.
    • (1991) J Mol Biol , vol.221 , pp. 327-346
    • Shoichet, B.K.1    Kuntz, I.D.2
  • 18
    • 0030248996 scopus 로고    scopus 로고
    • Low-resolution docking: prediction of complexes for underdetermined structures
    • Vakser IA. Low-resolution docking: prediction of complexes for underdetermined structures. Biopolymers 1996;39:455-464.
    • (1996) Biopolymers , vol.39 , pp. 455-464
    • Vakser, I.A.1
  • 19
    • 0034663658 scopus 로고    scopus 로고
    • Scoring docked conformations generated by rigid-body protein-protein docking
    • Camacho CJ, Gatchell DW, Kimura SR, Vajda S. Scoring docked conformations generated by rigid-body protein-protein docking. Proteins 2000;40:525-537.
    • (2000) Proteins , vol.40 , pp. 525-537
    • Camacho, C.J.1    Gatchell, D.W.2    Kimura, S.R.3    Vajda, S.4
  • 20
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • Gabb HA, Jackson RM, Sternberg MJ. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997;272:106-120.
    • (1997) J Mol Biol , vol.272 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.3
  • 21
  • 22
    • 0344980720 scopus 로고    scopus 로고
    • Combination of scoring functions improves discrimination in protein-protein docking
    • Murphy J, Gatchell DW, Prasad JC, Vajda S. Combination of scoring functions improves discrimination in protein-protein docking. Proteins 2003;53:840-854.
    • (2003) Proteins , vol.53 , pp. 840-854
    • Murphy, J.1    Gatchell, D.W.2    Prasad, J.C.3    Vajda, S.4
  • 23
    • 55749085508 scopus 로고    scopus 로고
    • DOCKGROUND protein-protein docking decoy set
    • Liu S, Gao Y, Vakser IA. DOCKGROUND protein-protein docking decoy set. Bioinformatics 2008;24:2634-2635.
    • (2008) Bioinformatics , vol.24 , pp. 2634-2635
    • Liu, S.1    Gao, Y.2    Vakser, I.A.3
  • 24
    • 33747840389 scopus 로고    scopus 로고
    • GRAMM-X public web server for protein-protein docking
    • Tovchigrechko A, Vakser IA. GRAMM-X public web server for protein-protein docking. Nucleic Acids Res 2006;34:W310-W314.
    • (2006) Nucleic Acids Res , vol.34
    • Tovchigrechko, A.1    Vakser, I.A.2
  • 28
    • 77957944014 scopus 로고    scopus 로고
    • Protein-protein docking benchmark version 4.0
    • Hwang H, Vreven T, Janin J, Weng Z. Protein-protein docking benchmark version 4.0. Proteins 2010;78:3111-3114.
    • (2010) Proteins , vol.78 , pp. 3111-3114
    • Hwang, H.1    Vreven, T.2    Janin, J.3    Weng, Z.4
  • 29
    • 0038526303 scopus 로고    scopus 로고
    • ZDOCK: an initial-stage protein-docking algorithm
    • Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003;52:80-87.
    • (2003) Proteins , vol.52 , pp. 80-87
    • Chen, R.1    Li, L.2    Weng, Z.3
  • 30
    • 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
  • 31
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, 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
  • 32
    • 78649531451 scopus 로고    scopus 로고
    • A large decoy set of protein-protein complexes produced by flexible docking
    • Launay G, Simonson T. A large decoy set of protein-protein complexes produced by flexible docking. J Comput Chem 2011;32:106-120.
    • (2011) J Comput Chem , vol.32 , pp. 106-120
    • Launay, G.1    Simonson, T.2
  • 33
    • 79954445193 scopus 로고    scopus 로고
    • dockYard-a repository to assist modeling of protein-protein docking
    • Mitra P, Pal D. dockYard-a repository to assist modeling of protein-protein docking. J Mol Model 2011;17:599-606.
    • (2011) J Mol Model , vol.17 , pp. 599-606
    • Mitra, P.1    Pal, D.2
  • 34
    • 33644848651 scopus 로고    scopus 로고
    • Optimal design of protein docking potentials: efficiency and limitations
    • Tobi D, Bahar I. Optimal design of protein docking potentials: efficiency and limitations. Proteins 2006;62:970-981.
    • (2006) Proteins , vol.62 , pp. 970-981
    • Tobi, D.1    Bahar, I.2
  • 35
    • 0026572775 scopus 로고
    • Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques
    • Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992;89:2195-2199.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 2195-2199
    • Katchalski-Katzir, E.1    Shariv, I.2    Eisenstein, M.3    Friesem, A.A.4    Aflalo, C.5    Vakser, I.A.6
  • 36
    • 33749020839 scopus 로고    scopus 로고
    • PIPER: an FFT-based protein docking program with pairwise potentials
    • Kozakov D, Brenke R, Comeau SR, Vajda S. PIPER: an FFT-based protein docking program with pairwise potentials. Proteins 2006;65:392-406.
    • (2006) Proteins , vol.65 , pp. 392-406
    • Kozakov, D.1    Brenke, R.2    Comeau, S.R.3    Vajda, S.4
  • 38
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • Smith GR, Sternberg MJ. 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
  • 39
    • 0345832301 scopus 로고    scopus 로고
    • ClusPro: an automated docking and discrimination method for the prediction of protein complexes
    • Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 2004;20:45-50.
    • (2004) Bioinformatics , vol.20 , pp. 45-50
    • Comeau, S.R.1    Gatchell, D.W.2    Vajda, S.3    Camacho, C.J.4
  • 41
    • 21644446565 scopus 로고    scopus 로고
    • Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function
    • Zhang C, Liu S, Zhou Y. Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function. Proteins 2005;60:314-318.
    • (2005) Proteins , vol.60 , pp. 314-318
    • Zhang, C.1    Liu, S.2    Zhou, Y.3
  • 42
    • 66149142757 scopus 로고    scopus 로고
    • Consensus scoring for enriching near-native structures from protein-protein docking decoys
    • Liang S, Meroueh SO, Wang G, Qiu C, Zhou Y. Consensus scoring for enriching near-native structures from protein-protein docking decoys. Proteins 2009;75:397-403.
    • (2009) Proteins , vol.75 , pp. 397-403
    • Liang, S.1    Meroueh, S.O.2    Wang, G.3    Qiu, C.4    Zhou, Y.5
  • 43
    • 0033562633 scopus 로고    scopus 로고
    • Use of pair potentials across protein interfaces in screening predicted docked complexes
    • Moont G, Gabb HA, Sternberg MJ. Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 1999;35:364-373.
    • (1999) Proteins , vol.35 , pp. 364-373
    • Moont, G.1    Gabb, H.A.2    Sternberg, M.J.3
  • 44
    • 0037340493 scopus 로고    scopus 로고
    • Development of unified statistical potentials describing protein-protein interactions
    • Lu H, Lu L, Skolnick J. Development of unified statistical potentials describing protein-protein interactions. Biophys J 2003;84:1895-1901.
    • (2003) Biophys J , vol.84 , pp. 1895-1901
    • Lu, H.1    Lu, L.2    Skolnick, J.3
  • 45
    • 58149152509 scopus 로고    scopus 로고
    • DARS (Decoys As the Reference State) potentials for protein-protein docking
    • Chuang GY, Kozakov D, Brenke R, Comeau SR, Vajda S. DARS (Decoys As the Reference State) potentials for protein-protein docking. Biophys J 2008;95:4217-4227.
    • (2008) Biophys J , vol.95 , pp. 4217-4227
    • Chuang, G.Y.1    Kozakov, D.2    Brenke, R.3    Comeau, S.R.4    Vajda, S.5
  • 47
    • 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
  • 48
    • 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
  • 50
    • 46449084711 scopus 로고    scopus 로고
    • An iterative knowledge-based scoring function for protein-protein recognition
    • Huang SY, Zou X. An iterative knowledge-based scoring function for protein-protein recognition. Proteins 2008;72:557-579.
    • (2008) Proteins , vol.72 , pp. 557-579
    • Huang, S.Y.1    Zou, X.2
  • 52
    • 77449134208 scopus 로고    scopus 로고
    • PIE-efficient filters and coarse grained potentials for unbound protein-protein docking
    • Ravikant DV, Elber R. PIE-efficient filters and coarse grained potentials for unbound protein-protein docking. Proteins 2010;78:400-419.
    • (2010) Proteins , vol.78 , pp. 400-419
    • Ravikant, D.V.1    Elber, R.2
  • 54
    • 80051880753 scopus 로고    scopus 로고
    • Energy design for protein-protein interactions
    • Ravikant DV, Elber R. Energy design for protein-protein interactions. J Chem Phys 2011;135:065102.
    • (2011) J Chem Phys , vol.135 , pp. 065102
    • Ravikant, D.V.1    Elber, R.2
  • 55
    • 17344380633 scopus 로고    scopus 로고
    • ICM-DISCO docking by global energy optimization with fully flexible side-chains
    • Fernandez-Recio J, Totrov M, Abagyan R. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins 2003;52:113-117.
    • (2003) Proteins , vol.52 , pp. 113-117
    • Fernandez-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 56
    • 36749006579 scopus 로고    scopus 로고
    • Docking and scoring protein complexes: CAPRI 3rd Edition
    • Lensink MF, Mendez R, Wodak SJ. Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins 2007;69:704-718.
    • (2007) Proteins , vol.69 , pp. 704-718
    • Lensink, M.F.1    Mendez, R.2    Wodak, S.J.3
  • 57
    • 21644469377 scopus 로고    scopus 로고
    • Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
    • Mendez R, Leplae R, Lensink MF, Wodak SJ. 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
  • 58
    • 23244436580 scopus 로고    scopus 로고
    • Optimal clustering for detecting near-native conformations in protein docking
    • Kozakov D, Clodfelter KH, Vajda S, Camacho CJ. Optimal clustering for detecting near-native conformations in protein docking. Biophys J 2005;89:867-875.
    • (2005) Biophys J , vol.89 , pp. 867-875
    • Kozakov, D.1    Clodfelter, K.H.2    Vajda, S.3    Camacho, C.J.4
  • 59
    • 0242299200 scopus 로고    scopus 로고
    • RDOCK: refinement of rigid-body protein docking predictions
    • Li L, Chen R, Weng Z. RDOCK: refinement of rigid-body protein docking predictions. Proteins 2003;53:693-707.
    • (2003) Proteins , vol.53 , pp. 693-707
    • Li, L.1    Chen, R.2    Weng, Z.3
  • 60
    • 34548317146 scopus 로고    scopus 로고
    • FireDock: Fast interaction refinement in molecular docking
    • Andrusier N, Nussinov R, Wolfson HJ. FireDock: Fast interaction refinement in molecular docking. Proteins 2007;69:139-159.
    • (2007) Proteins , vol.69 , pp. 139-159
    • Andrusier, N.1    Nussinov, R.2    Wolfson, H.J.3
  • 61
    • 47349119911 scopus 로고    scopus 로고
    • Discrimination of near-native structures in protein-protein docking by testing the stability of local minima
    • Kozakov D, Schueler-Furman O, Vajda S. Discrimination of near-native structures in protein-protein docking by testing the stability of local minima. Proteins 2008;72:993-1004.
    • (2008) Proteins , vol.72 , pp. 993-1004
    • Kozakov, D.1    Schueler-Furman, O.2    Vajda, S.3


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