메뉴 건너뛰기




Volumn 78, Issue 15, 2010, Pages 3096-3103

MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19

Author keywords

CAPRI experiments; Molecular docking; Protein protein interaction; Reduced model; Scoring function

Indexed keywords

ALGORITHM; ARTICLE; CONTROLLED STUDY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SCORING SYSTEM;

EID: 77957934483     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22797     Document Type: Article
Times cited : (63)

References (63)
  • 1
    • 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
  • 2
    • 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
  • 3
    • 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, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002;47:409-43.
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 4
    • 0347755444 scopus 로고    scopus 로고
    • Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking
    • Schneidman-Duhovny D, Nussinov R, Wolfson HJ. Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking. Curr Med Chem 2004;11:91-107.
    • (2004) Curr Med Chem , vol.11 , pp. 91-107
    • Schneidman-Duhovny, D.1    Nussinov, R.2    Wolfson, H.J.3
  • 5
    • 33646472024 scopus 로고    scopus 로고
    • High-resolution protein-protein docking
    • Gray JJ. High-resolution protein-protein docking. Curr Opin Struct Biol 2006;16:183-193.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 183-193
    • Gray, J.J.1
  • 7
    • 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
  • 8
    • 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
  • 11
    • 34250877416 scopus 로고    scopus 로고
    • Protein docking using surface matching and supervised machine learning
    • Bordner AJ, Gorin AA. Protein docking using surface matching and supervised machine learning. Proteins 2007;68:488-502.
    • (2007) Proteins , vol.68 , pp. 488-502
    • Bordner, A.J.1    Gorin, A.A.2
  • 12
    • 0026310932 scopus 로고
    • Soft docking: matching of molecular surface cubes
    • Jiang F, Kim SH. Soft docking: matching of molecular surface cubes. J Mol Biol 1991;219:79-102.
    • (1991) J Mol Biol , vol.219 , pp. 79-102
    • Jiang, F.1    Kim, S.H.2
  • 13
    • 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
  • 15
    • 84986522918 scopus 로고
    • ICM - A new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation
    • Abagyan R, Totrov M, Kuznetsov D. ICM - A new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comput Chem 1994;15:488-506.
    • (1994) J Comput Chem , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, M.2    Kuznetsov, D.3
  • 16
    • 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
  • 17
    • 0038583687 scopus 로고    scopus 로고
    • Protein-protein docking with a reduced protein model accounting for side-chain flexibility
    • Zacharias M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci 2003;12:1271-1282.
    • (2003) Protein Sci , vol.12 , pp. 1271-1282
    • Zacharias, M.1
  • 18
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: a protein-protein docking approach based on biochemical or biophysical information
    • Dominguez C, Boelens R, Bonvin AM. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 2003;125:1731-1737.
    • (2003) J Am Chem Soc , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.3
  • 19
    • 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
  • 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
    • 0031296607 scopus 로고    scopus 로고
    • Evaluation of GRAMM low-resolution docking methodology on the hemagglutininantibody complex
    • Vakser IA. Evaluation of GRAMM low-resolution docking methodology on the hemagglutininantibody complex. Proteins 1997;Suppl 1:226-230.
    • (1997) Proteins , Issue.SUPPL 1 , pp. 226-230
    • Vakser, I.A.1
  • 23
    • 0038185277 scopus 로고    scopus 로고
    • A novel shape complementarity scoring function for protein-protein docking
    • Chen R, Weng ZP. A novel shape complementarity scoring function for protein-protein docking. Proteins 2003;51:397-408.
    • (2003) Proteins , vol.51 , pp. 397-408
    • Chen, R.1    Weng, Z.P.2
  • 25
    • 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
  • 26
    • 33645961330 scopus 로고    scopus 로고
    • Flexible protein-protein docking
    • Bonvin AM. Flexible protein-protein docking. Curr Opin Struct Biol 2006;16:194-200.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 194-200
    • Bonvin, A.M.1
  • 27
    • 46449084711 scopus 로고    scopus 로고
    • An iterative knowledge-based scoring function for protein-protein recognition
    • Huang S-Y, 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
  • 28
    • 33846000313 scopus 로고    scopus 로고
    • Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking
    • Huang S-Y, Zou X. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins 2007;66:399-421.
    • (2007) Proteins , vol.66 , pp. 399-421
    • Huang, S.-Y.1    Zou, X.2
  • 29
    • 33845923184 scopus 로고    scopus 로고
    • Efficient molecular docking of NMR structures: application to HIV-1 protease
    • Huang S-Y, Zou X. Efficient molecular docking of NMR structures: application to HIV-1 protease. Protein Sci 2007;16:43-51.
    • (2007) Protein Sci , vol.16 , pp. 43-51
    • Huang, S.-Y.1    Zou, X.2
  • 31
    • 21644469377 scopus 로고    scopus 로고
    • Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
    • Méndez 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
    • Méndez, R.1    Leplae, R.2    Lensink, M.F.3    Wodak, S.J.4
  • 32
    • 36749006579 scopus 로고    scopus 로고
    • Docking and scoring protein complexes: CAPRI 3rd edition
    • Lensink MF, Wodak SJ, Méndez R. Docking and scoring protein complexes: CAPRI 3rd edition. Proteins 2007;69:704-718.
    • (2007) Proteins , vol.69 , pp. 704-718
    • Lensink, M.F.1    Wodak, S.J.2    Méndez, R.3
  • 33
    • 0028109886 scopus 로고
    • Conservation and prediction of solvent accessibility in protein families
    • Rost B, Sander C. Conservation and prediction of solvent accessibility in protein families. Proteins 1994;20:216-226.
    • (1994) Proteins , vol.20 , pp. 216-226
    • Rost, B.1    Sander, C.2
  • 34
    • 33750555073 scopus 로고    scopus 로고
    • An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials
    • Huang S-Y, Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials. J Comput Chem 2006;27:1865-1875.
    • (2006) J Comput Chem , vol.27 , pp. 1865-1875
    • Huang, S.-Y.1    Zou, X.2
  • 35
    • 33750574927 scopus 로고    scopus 로고
    • An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function
    • Huang S-Y, Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. J Comput Chem 2006;27:1876-1882.
    • (2006) J Comput Chem , vol.27 , pp. 1876-1882
    • Huang, S.-Y.1    Zou, X.2
  • 38
    • 0038526303 scopus 로고    scopus 로고
    • ZDOCK: an initial-stage protein-docking algorithm
    • Chen R, Li L, Weng ZP. 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.P.3
  • 39
    • 45649084937 scopus 로고    scopus 로고
    • Structural and mutational analyses of the interaction between the barley alpha-amylase/subtilisin inhibitor and the subtilisin savinase reveal a novel mode of inhibition
    • Micheelsen PO, Vévodová J, De Maria L, Ostergaard PR, Friis EP, Wilson K, Skjøt M. Structural and mutational analyses of the interaction between the barley alpha-amylase/subtilisin inhibitor and the subtilisin savinase reveal a novel mode of inhibition. J Mol Biol 2008;380:681-690.
    • (2008) J Mol Biol , vol.380 , pp. 681-690
    • Micheelsen, P.O.1    Vévodová, J.2    De Maria, L.3    Ostergaard, P.R.4    Friis, E.P.5    Wilson, K.6    Skjøt, M.7
  • 40
    • 0026501813 scopus 로고
    • Crystal structure of the alkaline proteinase Savinase from Bacillus lentus at 1.4 Å resolution
    • Betzel C, Klupsch S, Papendorf G, Hastrup S, Branner S, Wilson KS. Crystal structure of the alkaline proteinase Savinase from Bacillus lentus at 1.4 Å resolution. J Mol Biol 1992;223:427-445.
    • (1992) J Mol Biol , vol.223 , pp. 427-445
    • Betzel, C.1    Klupsch, S.2    Papendorf, G.3    Hastrup, S.4    Branner, S.5    Wilson, K.S.6
  • 41
    • 0032524130 scopus 로고    scopus 로고
    • Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution
    • Vallée F, Kadziola A, Bourne Y, Juy M, Rodenburg KW, Svensson B, Haser R. Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution. Structure 1998;6:649-659.
    • (1998) Structure , vol.6 , pp. 649-659
    • Vallée, F.1    Kadziola, A.2    Bourne, Y.3    Juy, M.4    Rodenburg, K.W.5    Svensson, B.6    Haser, R.7
  • 43
    • 0035866566 scopus 로고    scopus 로고
    • Differences in the specificities of the highly alkalophilic proteinases Savinase and Esperase imposed by changes in the rigidity and geometry of the substrate binding sites
    • Georgieva DN, Stoeva S, Voelter W, Genov N, Betzel C. Differences in the specificities of the highly alkalophilic proteinases Savinase and Esperase imposed by changes in the rigidity and geometry of the substrate binding sites. Arch Biochem Biophys 2001;387:197- 201.
    • (2001) Arch Biochem Biophys , vol.387 , pp. 197-201
    • Georgieva, D.N.1    Stoeva, S.2    Voelter, W.3    Genov, N.4    Betzel, C.5
  • 44
    • 17644379997 scopus 로고    scopus 로고
    • 2005. Mutational analysis of target enzyme recognition of the b-trefoil fold barley aamylase/subtilisin inhibitor
    • Bøsager BC, Nielsen PK, Abou Hachem M, Fukuda K, Præorius-Ibba M, Svensson B. 2005. Mutational analysis of target enzyme recognition of the b-trefoil fold barley aamylase/subtilisin inhibitor. J Biol Chem 2005;280:14855-14864.
    • (2005) J Biol Chem , vol.280 , pp. 14855-14864
    • Bøsager, B.C.1    Nielsen, P.K.2    Abou Hachem, M.3    Fukuda, K.4    Præorius-Ibba, M.5    Svensson, B.6
  • 45
    • 0037188507 scopus 로고    scopus 로고
    • Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction
    • Xiang Z, Soto CS, Honig B. Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proc Natl Acad Sci USA 2002;99:7432-7437.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 7432-7437
    • Xiang, Z.1    Soto, C.S.2    Honig, B.3
  • 47
    • 1642529580 scopus 로고    scopus 로고
    • Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site
    • Das K, Acton T, Chiang Y, Shih L, Arnold E, Montelione GT. Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site. Proc Natl Acad Sci USA 2004;101:4041-4046.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 4041-4046
    • Das, K.1    Acton, T.2    Chiang, Y.3    Shih, L.4    Arnold, E.5    Montelione, G.T.6
  • 52
    • 23644438026 scopus 로고    scopus 로고
    • Structural basis for the activation of cholera toxin by human ARF6-GTP
    • O'Neal CJ, Jobling MG, Holmes RK, Hol WG. Structural basis for the activation of cholera toxin by human ARF6-GTP. Science 2005;309:1093-1096.
    • (2005) Science , vol.309 , pp. 1093-1096
    • O'Neal, C.J.1    Jobling, M.G.2    Holmes, R.K.3    Hol, W.G.4
  • 53
    • 0026331267 scopus 로고
    • X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil
    • O'shea EK, Klemm JD, Kim PS, Alber T. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 1991;254:539-544.
    • (1991) Science , vol.254 , pp. 539-544
    • O'shea, E.K.1    Klemm, J.D.2    Kim, P.S.3    Alber, T.4
  • 55
    • 21044433466 scopus 로고    scopus 로고
    • Centaurin-alpha1 interacts directly with kinesin motor protein KIF13B
    • Venkateswarlu K, Hanada T, Chishti AH. Centaurin-alpha1 interacts directly with kinesin motor protein KIF13B. J Cell Sci 2005;118:2471-2484.
    • (2005) J Cell Sci , vol.118 , pp. 2471-2484
    • Venkateswarlu, K.1    Hanada, T.2    Chishti, A.H.3
  • 56
    • 70350355110 scopus 로고    scopus 로고
    • The ternary structure of double-headed arrowhead protease inhibitor API-A complexed with two trypsins reveals a novel reactive site conformation
    • Bao R, Zhou ZC, Jiang C, Lin SX, Chi CW, Chen Y. The ternary structure of double-headed arrowhead protease inhibitor API-A complexed with two trypsins reveals a novel reactive site conformation. J Biol Chem 2009;284:26676-26684
    • (2009) J Biol Chem , vol.284 , pp. 26676-26684
    • Bao, R.1    Zhou, Z.C.2    Jiang, C.3    Lin, S.X.4    Chi, C.W.5    Chen, Y.6
  • 57
    • 0028980848 scopus 로고
    • Episelection: novel Ki approximately nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface
    • Katz BA, Finer-Moore J, Mortezaei R, Rich DH, Stroud RM. Episelection: novel Ki approximately nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface. Biochemistry 1995;34:8264-8280.
    • (1995) Biochemistry , vol.34 , pp. 8264-8280
    • Katz, B.A.1    Finer-Moore, J.2    Mortezaei, R.3    Rich, D.H.4    Stroud, R.M.5
  • 58
    • 0016318618 scopus 로고
    • Mode of action of soybean trypsin inhibitor (Kunitz) as a model for specific protein-protein interactions
    • Blow DM, Janin J, Sweet RM. Mode of action of soybean trypsin inhibitor (Kunitz) as a model for specific protein-protein interactions. Nature 1974;249:54-57.
    • (1974) Nature , vol.249 , pp. 54-57
    • Blow, D.M.1    Janin, J.2    Sweet, R.M.3
  • 59
    • 0016291686 scopus 로고
    • Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II. Crystallographic refinement at 1. 9 A resolution
    • Huber R, Kukla D, Bode W, Schwager P, Bartels K, Deisenhofer J, Steigemann W. Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II. Crystallographic refinement at 1.9 A resolution. J Mol Biol 1974;89:73-101.
    • (1974) J Mol Biol , vol.89 , pp. 73-101
    • Huber, R.1    Kukla, D.2    Bode, W.3    Schwager, P.4    Bartels, K.5    Deisenhofer, J.6    Steigemann, W.7
  • 61
    • 0034283147 scopus 로고    scopus 로고
    • Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes
    • Kühlmann UC, Pommer AJ, Moore GR, James R, Kleanthous C. Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes. J Mol Biol 2000;301:1163-1178.
    • (2000) J Mol Biol , vol.301 , pp. 1163-1178
    • Kühlmann, U.C.1    Pommer, A.J.2    Moore, G.R.3    James, R.4    Kleanthous, C.5
  • 62
    • 77953593958 scopus 로고    scopus 로고
    • Self-association of TPR domains: Lessons learned from a designed, consensus-based TPR oligomer
    • Krachler AM, Sharma A, Kleanthous C. Self-association of TPR domains: Lessons learned from a designed, consensus-based TPR oligomer. Proteins 2010;78:2131-2143.
    • (2010) Proteins , vol.78 , pp. 2131-2143
    • Krachler, A.M.1    Sharma, A.2    Kleanthous, C.3
  • 63
    • 0037648552 scopus 로고    scopus 로고
    • Design of stable alpha-helical arrays from an idealized TPR motif
    • Main ER, Xiong Y, Cocco MJ, D'Andrea L, Regan L. Design of stable alpha-helical arrays from an idealized TPR motif. Structure 2003;11:497-508.
    • (2003) Structure , vol.11 , pp. 497-508
    • Main, E.R.1    Xiong, Y.2    Cocco, M.J.3    D'Andrea, L.4    Regan, L.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.