메뉴 건너뛰기




Volumn 81, Issue 12, 2013, Pages 2175-2182

Performance of ZDOCK in CAPRI rounds 20-26

Author keywords

Complexes; IRAD; Protein protein docking; Protein protein interaction; ZRANK

Indexed keywords

FERREDOXIN; HEMAGGLUTININ; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE; ZINOSTATIN; BACTERIAL PROTEIN; PROTEIN; PROTEIN BINDING; VIRUS PROTEIN;

EID: 84888288501     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24432     Document Type: Article
Times cited : (22)

References (49)
  • 2
    • 0037561868 scopus 로고    scopus 로고
    • ZDOCK predictions for the CAPRI challenge
    • Chen R, Tong W, Mintseris J, Li L, Weng Z. ZDOCK predictions for the CAPRI challenge. Proteins 2003;52(1):68-73.
    • (2003) Proteins , vol.52 , Issue.1 , pp. 68-73
    • Chen, R.1    Tong, W.2    Mintseris, J.3    Li, L.4    Weng, Z.5
  • 5
    • 77957951743 scopus 로고    scopus 로고
    • Performance of ZDOCK and ZRANK in CAPRI rounds 13-19
    • Hwang H, Vreven T, Pierce BG, Hung J-H, Weng Z. Performance of ZDOCK and ZRANK in CAPRI rounds 13-19. Proteins 2010;78(15):3104-3110.
    • (2010) Proteins , vol.78 , Issue.15 , pp. 3104-3110
    • Hwang, H.1    Vreven, T.2    Pierce, B.G.3    Hung, J.-H.4    Weng, Z.5
  • 6
    • 0038185277 scopus 로고    scopus 로고
    • A novel shape complementarity scoring function for protein-protein docking
    • Chen R, Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins 2003;51(3):397-408.
    • (2003) Proteins , vol.51 , Issue.3 , pp. 397-408
    • Chen, R.1    Weng, Z.2
  • 7
    • 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(1):80-87.
    • (2003) Proteins , vol.52 , Issue.1 , pp. 80-87
    • Chen, R.1    Li, L.2    Weng, Z.3
  • 8
    • 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(3):511-520.
    • (2007) Proteins , vol.69 , Issue.3 , pp. 511-520
    • Mintseris, J.1    Pierce, B.2    Wiehe, K.3    Anderson, R.4    Chen, R.5    Weng, Z.6
  • 9
    • 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(4):1078-1086.
    • (2007) Proteins , vol.67 , Issue.4 , pp. 1078-1086
    • Pierce, B.1    Weng, Z.2
  • 10
    • 84860388898 scopus 로고    scopus 로고
    • Integrating atom-based and residue-based scoring functions for protein-protein docking
    • Vreven T, Hwang H, Weng Z. Integrating atom-based and residue-based scoring functions for protein-protein docking. Protein Sci 2011;20(9):1576-1586.
    • (2011) Protein Sci , vol.20 , Issue.9 , pp. 1576-1586
    • Vreven, T.1    Hwang, H.2    Weng, Z.3
  • 11
    • 44949117092 scopus 로고    scopus 로고
    • A combination of rescoring and refinement significantly improves protein docking performance
    • Pierce B, Weng Z. A combination of rescoring and refinement significantly improves protein docking performance. Proteins 2008;72(1):270-279.
    • (2008) Proteins , vol.72 , Issue.1 , pp. 270-279
    • Pierce, B.1    Weng, Z.2
  • 12
    • 61449234107 scopus 로고    scopus 로고
    • Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC
    • Haidar JN, Pierce B, Yu Y, Tong W, Li M, Weng Z. Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC. Proteins 2009;74(4):948-960.
    • (2009) Proteins , vol.74 , Issue.4 , pp. 948-960
    • Haidar, J.N.1    Pierce, B.2    Yu, Y.3    Tong, W.4    Li, M.5    Weng, Z.6
  • 13
    • 84857428250 scopus 로고    scopus 로고
    • Prediction of protein-protein binding free energies
    • Vreven T, Hwang H, Pierce BG, Weng Z. Prediction of protein-protein binding free energies. Protein Sci 2012;21(3):396-404.
    • (2012) Protein Sci , vol.21 , Issue.3 , pp. 396-404
    • Vreven, T.1    Hwang, H.2    Pierce, B.G.3    Weng, Z.4
  • 14
    • 80052903046 scopus 로고    scopus 로고
    • Accelerating protein docking in ZDOCK using an advanced 3D convolution library
    • Pierce BG, Hourai Y, Weng Z. Accelerating protein docking in ZDOCK using an advanced 3D convolution library. PLoS ONE 2011;6(9):e24657.
    • (2011) PLoS ONE , vol.6 , Issue.9
    • Pierce, B.G.1    Hourai, Y.2    Weng, Z.3
  • 15
    • 84874328246 scopus 로고    scopus 로고
    • Exploring angular distance in protein-protein docking algorithms
    • Vreven T, Hwang H, Weng Z. Exploring angular distance in protein-protein docking algorithms. PLoS ONE 2013;8(2):e56645.
    • (2013) PLoS ONE , vol.8 , Issue.2
    • Vreven, T.1    Hwang, H.2    Weng, Z.3
  • 16
    • 84888303955 scopus 로고    scopus 로고
    • Binding interface prediction by combining protein-protein docking results
    • Hwang H, Vreven T, Weng Z. Binding interface prediction by combining protein-protein docking results. Proteins 2013.
    • (2013) Proteins
    • Hwang, H.1    Vreven, T.2    Weng, Z.3
  • 17
    • 79953040045 scopus 로고    scopus 로고
    • CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK
    • De Vries SJ, Bonvin AMJJ. CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK. PLoS ONE 2011;6(3):e17695.
    • (2011) PLoS ONE , vol.6 , Issue.3
    • De Vries, S.J.1    Bonvin, A.M.J.J.2
  • 18
    • 1542390499 scopus 로고    scopus 로고
    • Identification of protein-protein interaction sites from docking energy landscapes
    • Fernandez-Recio J, Totrov M, Abagyan R. Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 2004;335(3):843-865.
    • (2004) J Mol Biol , vol.335 , Issue.3 , pp. 843-865
    • Fernandez-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 19
    • 84882901819 scopus 로고    scopus 로고
    • Ranking multiple docking solutions based on the conservation of inter-residue contacts
    • 201381
    • Oliva R, Vangone A, Cavallo L. Ranking multiple docking solutions based on the conservation of inter-residue contacts. Proteins 201381(9):1571-1584.
    • Proteins , Issue.9 , pp. 1571-1584
    • Oliva, R.1    Vangone, A.2    Cavallo, L.3
  • 20
    • 0035882570 scopus 로고    scopus 로고
    • Prediction of protein interaction sites from sequence profile and residue neighbor list
    • Zhou H-X, Shan Y. Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 2001;44(3):336-343.
    • (2001) Proteins , vol.44 , Issue.3 , pp. 336-343
    • Zhou, H.-X.1    Shan, Y.2
  • 21
    • 36749082073 scopus 로고    scopus 로고
    • A holistic approach to protein docking
    • Qin S, Zhou H-X. A holistic approach to protein docking. Proteins 2007;69(4):743-749.
    • (2007) Proteins , vol.69 , Issue.4 , pp. 743-749
    • Qin, S.1    Zhou, H.-X.2
  • 23
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray J, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl C, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331(1):281-299.
    • (2003) J Mol Biol , vol.331 , Issue.1 , pp. 281-299
    • Gray, J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.6    Baker, D.7
  • 25
  • 29
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the Web: a case study using the Phyre server
    • Kelley LA, Sternberg MJE. Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 2009;4(3):363-371.
    • (2009) Nat Protoc , vol.4 , Issue.3 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.E.2
  • 30
    • 0035747672 scopus 로고    scopus 로고
    • Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM
    • Suppl
    • Bates PA, Kelley LA, MacCallum RM, Sternberg MJ. Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins 2001;Suppl 5:39-46.
    • (2001) Proteins , vol.5 , pp. 39-46
    • Bates, P.A.1    Kelley, L.A.2    MacCallum, R.M.3    Sternberg, M.J.4
  • 32
    • 58049215418 scopus 로고    scopus 로고
    • Structural consequences of effector protein complex formation in a diiron hydroxylase
    • Bailey LJ, McCoy JG, Phillips GN, Fox BG. Structural consequences of effector protein complex formation in a diiron hydroxylase. Proc Natl Acad Sci USA 2008;105(49):19194-19198.
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.49 , pp. 19194-19198
    • Bailey, L.J.1    McCoy, J.G.2    Phillips, G.N.3    Fox, B.G.4
  • 34
    • 33846687102 scopus 로고    scopus 로고
    • Redox and functional analysis of the Rieske ferredoxin component of the toluene 4-monooxygenase
    • Elsen NL, Moe LA, McMartin LA, Fox BG. Redox and functional analysis of the Rieske ferredoxin component of the toluene 4-monooxygenase. Biochemistry 2007;46(4):976-986.
    • (2007) Biochemistry , vol.46 , Issue.4 , pp. 976-986
    • Elsen, N.L.1    Moe, L.A.2    McMartin, L.A.3    Fox, B.G.4
  • 35
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234(3):779-815.
    • (1993) J Mol Biol , vol.234 , Issue.3 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 39
    • 0037006986 scopus 로고    scopus 로고
    • High-resolution crystal structures of the lectin-like xylan binding domain from Streptomyces lividans xylanase 10A with bound substrates reveal a novel mode of xylan binding
    • Notenboom V, Boraston AB, Williams SJ, Kilburn DG, Rose DR. High-resolution crystal structures of the lectin-like xylan binding domain from Streptomyces lividans xylanase 10A with bound substrates reveal a novel mode of xylan binding. Biochemistry 2002;41(13):4246-4254.
    • (2002) Biochemistry , vol.41 , Issue.13 , pp. 4246-4254
    • Notenboom, V.1    Boraston, A.B.2    Williams, S.J.3    Kilburn, D.G.4    Rose, D.R.5
  • 41
    • 18844453949 scopus 로고    scopus 로고
    • Prediction of multimolecular assemblies by multiple docking
    • Inbar Y, Benyamini H, Nussinov R, Wolfson H. Prediction of multimolecular assemblies by multiple docking. J Mol Biol 2005;349(2):435-447.
    • (2005) J Mol Biol , vol.349 , Issue.2 , pp. 435-447
    • Inbar, Y.1    Benyamini, H.2    Nussinov, R.3    Wolfson, H.4
  • 42
    • 77955371384 scopus 로고    scopus 로고
    • Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server
    • Karaca E, Melquiond ASJ, De Vries SJ, Kastritis PL, Bonvin AMJJ. Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server. Mol Cell Proteomics 2010;9(8):1784-1794.
    • (2010) Mol Cell Proteomics , vol.9 , Issue.8 , pp. 1784-1794
    • Karaca, E.1    Melquiond, A.S.J.2    De Vries, S.J.3    Kastritis, P.L.4    Bonvin, A.M.J.J.5
  • 43
    • 78349304669 scopus 로고    scopus 로고
    • Design, production and molecular structure of a new family of artificial alpha-helicoidal repeat proteins (αRep) based on thermostable HEAT-like repeats
    • Urvoas A, Guellouz A, Valerio-Lepiniec M, Graille M, Durand D, Desravines DC, van Tilbeurgh H, Desmadril M, Minard P. Design, production and molecular structure of a new family of artificial alpha-helicoidal repeat proteins (αRep) based on thermostable HEAT-like repeats. J Mol Biol 2010;404(2):307-327.
    • (2010) J Mol Biol , vol.404 , Issue.2 , pp. 307-327
    • Urvoas, A.1    Guellouz, A.2    Valerio-Lepiniec, M.3    Graille, M.4    Durand, D.5    Desravines, D.C.6    van Tilbeurgh, H.7    Desmadril, M.8    Minard, P.9
  • 44
    • 0037195144 scopus 로고    scopus 로고
    • A simple physical model for binding energy hot spots in protein-protein complexes
    • Kortemme T, Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci USA 2002;99(22):14116-14121.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.22 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 48
    • 46449139781 scopus 로고    scopus 로고
    • Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions
    • Yang Y, Zhou Y. Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions. Protein Sci 2008;17(7):1212-1219.
    • (2008) Protein Sci , vol.17 , Issue.7 , pp. 1212-1219
    • Yang, Y.1    Zhou, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.