메뉴 건너뛰기




Volumn 53, Issue 3, 2003, Pages 693-707

RDOCK: Refinement of Rigid-body Protein Docking Predictions

Author keywords

Binding free energy; Docking refinement; Energy minimization; Neutralized ionic side chains; Protein docking; RDOCK

Indexed keywords

ALGORITHM; ARTICLE; AUTOMATION; ELECTRICITY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DOCKING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RIGID BODY DOCKING ALGORITHM; RIGID BODY PROTEIN DOCKING; SCORING SYSTEM; ZDOCK 2.1 ALGORITHM; ZDOCK ALGORITHM;

EID: 0242299200     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10460     Document Type: Article
Times cited : (288)

References (42)
  • 1
    • 0016694062 scopus 로고
    • Hemoglobin interaction in sickle cell fibers, I: Theoretical approaches to the molecular contacts
    • Levinthal C, Wodak SJ, Kahn P, Dadivanian AK. Hemoglobin interaction in sickle cell fibers, I: theoretical approaches to the molecular contacts. Proc Natl Acad Sci USA 1975;72:1330-1334.
    • (1975) Proc Natl Acad Sci USA , vol.72 , pp. 1330-1334
    • Levinthal, C.1    Wodak, S.J.2    Kahn, P.3    Dadivanian, A.K.4
  • 2
    • 0018165127 scopus 로고
    • Computer analysis of protein-protein interaction
    • Wodak SJ, Janin J. Computer analysis of protein-protein interaction. J Mol Biol 1978;124:323-342.
    • (1978) J Mol Biol , vol.124 , pp. 323-342
    • Wodak, S.J.1    Janin, J.2
  • 4
    • 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
  • 5
    • 0242338384 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. Proteins 1997;S1:226-230.
    • (1997) Proteins , vol.S1 , pp. 226-230
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.3
  • 6
    • 0031296607 scopus 로고    scopus 로고
    • Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex
    • Vakser IA. Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex. Proteins 1997; (Suppl 1):226-30.
    • (1997) Proteins , Issue.SUPPL. 1 , pp. 226-230
    • Vakser, I.A.1
  • 7
    • 0034193510 scopus 로고    scopus 로고
    • Protein docking using spherical polar Fourier correlations
    • Ritchie DW, Kemp GJ. Protein docking using spherical polar Fourier correlations. Proteins 2000;39:178-194.
    • (2000) Proteins , vol.39 , pp. 178-194
    • Ritchie, D.W.1    Kemp, G.J.2
  • 8
    • 0034212826 scopus 로고    scopus 로고
    • BiGGER: A new (soft) docking algorithm for predicting protein interactions
    • Palma PN, Krippahl L, Wampler JE, Moura JJ. BIGGER: A new (soft) docking algorithm for predicting protein interactions. Proteins 2000;39:372-384.
    • (2000) Proteins , vol.39 , pp. 372-384
    • Palma, P.N.1    Krippahl, L.2    Wampler, J.E.3    Moura, J.J.4
  • 9
    • 0034332970 scopus 로고    scopus 로고
    • DARWIN: A program for docking flexible molecules
    • Taylor JS, Burnett RM. 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
  • 12
    • 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
  • 13
    • 0037093643 scopus 로고    scopus 로고
    • Docking unbound proteins using shape complementarity, desolvation, and electrostatics
    • Chen R, Weng Z. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 2002;47:281-294.
    • (2002) Proteins , vol.47 , pp. 281-294
    • Chen, R.1    Weng, Z.2
  • 14
    • 0036149480 scopus 로고    scopus 로고
    • Soft protein-protein docking in internal coordinates
    • Fernandez-Recio J, Totrov M, Abagyan R. Soft protein-protein docking in internal coordinates. Protein Sci 2002;11:280-291.
    • (2002) Protein Sci , vol.11 , pp. 280-291
    • Fernandez-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 15
    • 0029019869 scopus 로고
    • A continuum model for protein-protein interactions: Application to the docking problem
    • Jackson RM, Sternberg MJE. A continuum model for protein-protein interactions: Application to the docking problem. J Mol Biol 1995;250:258-275.
    • (1995) J Mol Biol , vol.250 , pp. 258-275
    • Jackson, R.M.1    Sternberg, M.J.E.2
  • 16
    • 0029933286 scopus 로고    scopus 로고
    • Prediction of protein complexes using empirical free energy functions
    • Weng Z, Vajda S, Delisi C. Prediction of protein complexes using empirical free energy functions. Protein Sci 1996;5:614-626.
    • (1996) Protein Sci , vol.5 , pp. 614-626
    • Weng, Z.1    Vajda, S.2    Delisi, C.3
  • 17
    • 0032512619 scopus 로고    scopus 로고
    • Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem
    • Jackson RM, Gabb HA, Sternberg MJ. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J Mol Biol 1998;276:265-285.
    • (1998) J Mol Biol , vol.276 , pp. 265-285
    • Jackson, R.M.1    Gabb, H.A.2    Sternberg, M.J.3
  • 18
    • 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
  • 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
    • 0035845563 scopus 로고    scopus 로고
    • Protein docking along smooth association pathways
    • Camacho CJ, Vajda S. Protein docking along smooth association pathways. Proc Natl Acad Sci USA 2001;98:10636-10641.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 10636-10641
    • Camacho, C.J.1    Vajda, S.2
  • 21
    • 0026319198 scopus 로고
    • Protein-protein recognition analyzed by docking simulation
    • Cherfils J, Duquerroy S, Janin J. Protein-protein recognition analyzed by docking simulation. Proteins 1991;11:271-280.
    • (1991) Proteins , vol.11 , pp. 271-280
    • Cherfils, J.1    Duquerroy, S.2    Janin, J.3
  • 22
    • 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
  • 23
    • 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
  • 24
    • 0026464639 scopus 로고
    • New algorithm to model protein-protein recognition based on surface complementarity applications to antibody-antigen docking
    • Walls PH, Sternberg MJE. New algorithm to model protein-protein recognition based on surface complementarity. applications to antibody-antigen docking. J Mol Biol 1992;228:277-297.
    • (1992) J Mol Biol , vol.228 , pp. 277-297
    • Walls, P.H.1    Sternberg, M.J.E.2
  • 25
    • 0027530108 scopus 로고
    • Protein docking algorithms: Simulating molecular recognition
    • Cherfils J, Janin J. Protein docking algorithms: simulating molecular recognition. Curr Opin Struct Biol 1993;3:265-269.
    • (1993) Curr Opin Struct Biol , vol.3 , pp. 265-269
    • Cherfils, J.1    Janin, J.2
  • 27
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg D, McLachlan AD. Solvation energy in protein folding and binding. Nature (London) 1986;319:199-203.
    • (1986) Nature (London) , vol.319 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 28
    • 0027166270 scopus 로고
    • Empirical scale of side-chain conformational entropy in protein folding
    • Pickett SD, Sternberg MJE. Empirical scale of side-chain conformational entropy in protein folding. J Mol Biol 1993;231:825-839.
    • (1993) J Mol Biol , vol.231 , pp. 825-839
    • Pickett, S.D.1    Sternberg, M.J.E.2
  • 29
    • 0023807627 scopus 로고
    • Structure of antibody hypervariable loops reproduced by a conformational search algorithm
    • Bruccoleri RE, Haber E, Novotny J. Structure of antibody hypervariable loops reproduced by a conformational search algorithm [published erratum appears in Nature 1988 Nov 17;336(6196): 266]. Nature 1988;335:564-568.
    • (1988) Nature , vol.335 , pp. 564-568
    • Bruccoleri, R.E.1    Haber, E.2    Novotny, J.3
  • 30
    • 0242338383 scopus 로고
    • published erratum appears, Nov 17
    • Bruccoleri RE, Haber E, Novotny J. Structure of antibody hypervariable loops reproduced by a conformational search algorithm [published erratum appears in Nature 1988 Nov 17;336(6196): 266]. Nature 1988;335:564-568.
    • (1988) Nature , vol.336 , Issue.6196 , pp. 266
  • 31
    • 0033566576 scopus 로고    scopus 로고
    • Examination of shape complementarity in docking of unbound proteins
    • Norel R, Petrey D, Wolfson HJ, 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
  • 32
    • 0028410583 scopus 로고
    • Detailed ab initio prediction of lysozymeantibody complex with 1.6 a accuracy
    • Totrov M, Abagyan R. Detailed ab initio prediction of lysozymeantibody complex with 1.6 A accuracy. Nat Struct Biol 1994;1:259-263.
    • (1994) Nat Struct Biol , vol.1 , pp. 259-263
    • Totrov, M.1    Abagyan, R.2
  • 33
    • 0242306855 scopus 로고    scopus 로고
    • Determination of atomic desolvation energies from the structures of crystallized proteins
    • Zhang C, Vasmatzis G, Cornette JL, DeLisi C. Determination of atomic desolvation energies from the structures of crystallized proteins. Proteins 1997;51:397-408.
    • (1997) Proteins , vol.51 , pp. 397-408
    • Zhang, C.1    Vasmatzis, G.2    Cornette, J.L.3    DeLisi, C.4
  • 34
    • 0242369759 scopus 로고    scopus 로고
    • A novel shape complementarity scoring function for protein-protein docking
    • Forthcoming
    • Chen R, Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins Forthcoming.
    • Proteins
    • Chen, R.1    Weng, Z.2
  • 35
    • 0242275046 scopus 로고    scopus 로고
    • ZDOCK: An initial-stage protein docking algorithm
    • Forthcoming
    • Chen R, Li L, Weng Z. ZDOCK: An initial-stage protein docking algorithm. Proteins Forthcoming.
    • Proteins
    • Chen, R.1    Li, L.2    Weng, Z.3
  • 38
    • 0029006770 scopus 로고
    • Comparison of methods for searching protein sequence databases
    • Pearson WR. Comparison of methods for searching protein sequence databases. Protein Sci 1995;4:1145-1160.
    • (1995) Protein Sci , vol.4 , pp. 1145-1160
    • Pearson, W.R.1
  • 39
    • 0036108486 scopus 로고    scopus 로고
    • Protein-protein docking with multiple residue conformations and residue substitutions
    • Lorber DM, Udo MK, Shoichet BK. Protein-protein docking with multiple residue conformations and residue substitutions. Protein Sci 2002;11:1393-1408.
    • (2002) Protein Sci , vol.11 , pp. 1393-1408
    • Lorber, D.M.1    Udo, M.K.2    Shoichet, B.K.3
  • 40
    • 0034560338 scopus 로고    scopus 로고
    • Discrimination of near-native protein structures from misfolded models by empirical free energy functions
    • Gatchell DW, Dennis S, Vajda S. Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins 2000;41:518-534.
    • (2000) Proteins , vol.41 , pp. 518-534
    • Gatchell, D.W.1    Dennis, S.2    Vajda, S.3
  • 41
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133-152.
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 42
    • 0033531959 scopus 로고    scopus 로고
    • Discrimination of the native from misfolded protein models with an energy function including implicit solvation
    • Lazaridis T, Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol 1999;288:477-487.
    • (1999) J Mol Biol , vol.288 , pp. 477-487
    • Lazaridis, T.1    Karplus, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.