메뉴 건너뛰기




Volumn 5, Issue 8, 2009, Pages

Pushing structural information into the yeast interactome by high-throughput protein docking experiments

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR BIOLOGY; POLYCHLORINATED BIPHENYLS; THROUGHPUT; YEAST;

EID: 70049112107     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000490     Document Type: Article
Times cited : (68)

References (63)
  • 5
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636.
    • (2006) Nature , vol.440 , pp. 631-636
    • Gavin, A.C.1    Aloy, P.2    Grandi, P.3    Krause, R.4    Boesche, M.5
  • 6
    • 33645453254 scopus 로고    scopus 로고
    • Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    • Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643.
    • (2006) Nature , vol.440 , pp. 637-643
    • Krogan, N.J.1    Cagney, G.2    Yu, H.3    Zhong, G.4    Guo, X.5
  • 9
    • 33847744247 scopus 로고    scopus 로고
    • How complete are current yeast and human protein-interaction networks?
    • Hart GT, Ramani AK, Marcotte EM (2006) How complete are current yeast and human protein-interaction networks? Genome Biol 7: 120.
    • (2006) Genome Biol , vol.7 , pp. 120
    • Hart, G.T.1    Ramani, A.K.2    Marcotte, E.M.3
  • 10
    • 49749117432 scopus 로고    scopus 로고
    • Contextual specificity in peptide-mediated protein interactions
    • Stein A, Aloy P (2008) Contextual specificity in peptide-mediated protein interactions. PLoS ONE 3: e2524.
    • (2008) PLoS ONE , vol.3
    • Stein, A.1    Aloy, P.2
  • 11
    • 44649187518 scopus 로고    scopus 로고
    • Incorporating high-throughput proteomics experiments into structural biology pipelines: Identification of the low-hanging fruits
    • Pache RA, Aloy P (2008) Incorporating high-throughput proteomics experiments into structural biology pipelines: identification of the low-hanging fruits. Proteomics 8: 1959-1964.
    • (2008) Proteomics , vol.8 , pp. 1959-1964
    • Pache, R.A.1    Aloy, P.2
  • 12
    • 0042386609 scopus 로고    scopus 로고
    • The relationship between sequence and interaction divergence in proteins
    • DOI 10.1016/j.jmb.2003.07.006
    • Aloy P, Ceulemans H, Stark A, Russell RB (2003) The relationship between sequence and interaction divergence in proteins. J Mol Biol 332: 989-998. (Pubitemid 37108793)
    • (2003) Journal of Molecular Biology , vol.332 , Issue.5 , pp. 989-998
    • Aloy, P.1    Ceulemans, H.2    Stark, A.3    Russell, R.B.4
  • 14
    • 33645961330 scopus 로고    scopus 로고
    • Flexible protein-protein docking
    • Bonvin AM (2006) Flexible protein-protein docking. Curr Opin Struct Biol 16: 194-200.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 194-200
    • Bonvin, A.M.1
  • 15
    • 33646472024 scopus 로고    scopus 로고
    • High-resolution protein-protein docking
    • Gray JJ (2006) High-resolution protein-protein docking. Curr Opin Struct Biol 16: 183-193.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 183-193
    • Gray, J.J.1
  • 16
    • 41949111630 scopus 로고    scopus 로고
    • Recent progress and future directions in protein-protein docking
    • Ritchie DW (2008) Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci 9: 1-15.
    • (2008) Curr Protein Pept Sci , vol.9 , pp. 1-15
    • Ritchie, D.W.1
  • 18
    • 0038021436 scopus 로고    scopus 로고
    • Assessment of blind predictions of protein-protein interactions: Current status of docking methods
    • DOI 10.1002/prot.10393
    • Mendez R, Leplae R, De Maria L, Wodak SJ (2003) Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 52: 51-67. (Pubitemid 36648851)
    • (2003) Proteins: Structure, Function and Genetics , vol.52 , Issue.1 , pp. 51-67
    • Mendez, R.1    Leplae, R.2    De Maria, L.3    Wodak, S.J.4
  • 20
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • Gabb HA, Jackson RM, Sternberg MJ (1997) Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 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
    • 0038526303 scopus 로고    scopus 로고
    • ZDOCK: An initial-stage protein-docking algorithm
    • Chen R, Li L, Weng Z (2003) ZDOCK: an initial-stage protein-docking algorithm. Proteins 52: 80-87.
    • (2003) Proteins , vol.52 , pp. 80-87
    • Chen, R.1    Li, L.2    Weng, Z.3
  • 22
    • 0037093643 scopus 로고    scopus 로고
    • Docking unbound proteins using shape complementarity, desolvation, and electrostatics
    • DOI 10.1002/prot.10092
    • Chen R, Weng Z (2002) Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 47: 281-294. (Pubitemid 34438678)
    • (2002) Proteins: Structure, Function and Genetics , vol.47 , Issue.3 , pp. 281-294
    • Chen, R.1    Weng, Z.2
  • 24
    • 0034193510 scopus 로고    scopus 로고
    • Protein docking using spherical polar Fourier correlations
    • Ritchie DW, Kemp GJ (2000) Protein docking using spherical polar Fourier correlations. Proteins 39: 178-194.
    • (2000) Proteins , vol.39 , pp. 178-194
    • Ritchie, D.W.1    Kemp, G.J.2
  • 25
    • 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, et al. (1992) Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci U S A 89: 2195-2199.
    • (1992) Proc Natl Acad Sci U S A , vol.89 , pp. 2195-2199
    • Katchalski-Katzir, E.1    Shariv, I.2    Eisenstein, M.3    Friesem, A.A.4    Aflalo, C.5
  • 26
    • 0036149480 scopus 로고    scopus 로고
    • Soft protein-protein docking in internal coordinates
    • DOI 10.1110/ps.19202
    • Fernandez-Recio J, Totrov M, Abagyan R (2002) Soft protein-protein docking in internal coordinates. Protein Sci 11: 280-291. (Pubitemid 34075791)
    • (2002) Protein Science , vol.11 , Issue.2 , pp. 280-291
    • Fernandez-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 29
    • 34250882254 scopus 로고    scopus 로고
    • pyDock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking
    • Cheng TM, Blundell TL, Fernandez-Recio J (2007) pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking. Proteins 68: 503-515.
    • (2007) Proteins , vol.68 , pp. 503-515
    • Cheng, T.M.1    Blundell, T.L.2    Fernandez-Recio, J.3
  • 31
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • DOI 10.1021/ja026939x
    • Dominguez C, Boelens R, Bonvin AM (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125: 1731-1737. (Pubitemid 36232568)
    • (2003) Journal of the American Chemical Society , vol.125 , Issue.7 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.J.J.3
  • 32
    • 21644437700 scopus 로고    scopus 로고
    • Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets
    • Camacho CJ (2005) Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets. Proteins 60: 245-251.
    • (2005) Proteins , vol.60 , pp. 245-251
    • Camacho, C.J.1
  • 33
    • 0038359596 scopus 로고    scopus 로고
    • Successful discrimination of protein interactions
    • Camacho CJ, Gatchell DW (2003) Successful discrimination of protein interactions. Proteins 52: 92-97.
    • (2003) Proteins , vol.52 , pp. 92-97
    • Camacho, C.J.1    Gatchell, D.W.2
  • 34
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • DOI 10.1016/S0022-2836(03)00670-3
    • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, et al. (2003) Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 331: 281-299. (Pubitemid 36870793)
    • (2003) Journal of Molecular Biology , vol.331 , Issue.1 , 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
  • 35
    • 21644435306 scopus 로고    scopus 로고
    • ATTRACT: Protein-protein docking in CAPRI using a reduced protein model
    • DOI 10.1002/prot.20566
    • Zacharias M (2005) ATTRACT: protein-protein docking in CAPRI using a reduced protein model. Proteins 60: 252-256. (Pubitemid 40934895)
    • (2005) Proteins: Structure, Function and Genetics , vol.60 , Issue.2 , pp. 252-256
    • Zacharias, M.1
  • 36
    • 1242270553 scopus 로고    scopus 로고
    • Protein-protein docking: Is the glass half-full or half-empty?
    • Vajda S, Camacho CJ (2004) Protein-protein docking: is the glass half-full or half-empty? Trends Biotechnol 22: 110-116.
    • (2004) Trends Biotechnol , vol.22 , pp. 110-116
    • Vajda, S.1    Camacho, C.J.2
  • 37
    • 21644458102 scopus 로고    scopus 로고
    • Classification of protein complexes based on docking difficulty
    • DOI 10.1002/prot.20554
    • Vajda S (2005) Classification of protein complexes based on docking difficulty. Proteins 60: 176-180. (Pubitemid 40934883)
    • (2005) Proteins: Structure, Function and Genetics , vol.60 , Issue.2 , pp. 176-180
    • Vajda, S.1
  • 39
    • 0038185277 scopus 로고    scopus 로고
    • A novel shape complementarity scoring function for protein-protein docking
    • DOI 10.1002/prot.10334
    • Chen R, Weng Z (2003) A novel shape complementarity scoring function for protein-protein docking. Proteins 51: 397-408. (Pubitemid 36528825)
    • (2003) Proteins: Structure, Function and Genetics , vol.51 , Issue.3 , pp. 397-408
    • Chen, R.1    Weng, Z.2
  • 40
    • 0031552370 scopus 로고    scopus 로고
    • Determination of atomic desolvation energies from the structures of crystallized proteins
    • DOI 10.1006/jmbi.1996.0859
    • Zhang C, Vasmatzis G, Cornette JL, DeLisi C (1997) Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol 267: 707-726. (Pubitemid 27170692)
    • (1997) Journal of Molecular Biology , vol.267 , Issue.3 , pp. 707-726
    • Zhang, C.1    Vasmatzis, G.2    Cornette, J.L.3    Delisi, C.4
  • 41
    • 18244392226 scopus 로고    scopus 로고
    • Optimizing protein representations with information theory
    • Mintseris J, Weng Z (2004) Optimizing protein representations with information theory. Genome Inform 15: 160-169.
    • (2004) Genome Inform , vol.15 , pp. 160-169
    • Mintseris, J.1    Weng, Z.2
  • 42
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • Canutescu AA, Shelenkov AA, Dunbrack RL Jr (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 12: 2001-2014.
    • (2003) Protein Sci , vol.12 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack Jr., R.L.3
  • 50
    • 51849139041 scopus 로고    scopus 로고
    • Alignment of protein structures in the presence of domain motions
    • Mosca R, Brannetti B, Schneider TR (2008) Alignment of protein structures in the presence of domain motions. BMC Bioinformatics 9: 352.
    • (2008) BMC Bioinformatics , vol.9 , pp. 352
    • Mosca, R.1    Brannetti, B.2    Schneider, T.R.3
  • 51
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. Embo J 5: 823-826.
    • (1986) Embo J , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 56
    • 33847317318 scopus 로고    scopus 로고
    • Inherent limitations in protein-protein docking procedures
    • DOI 10.1093/bioinformatics/btl524
    • Kowalsman N, Eisenstein M (2007) Inherent limitations in protein-protein docking procedures. Bioinformatics 23: 421-426. (Pubitemid 46323122)
    • (2007) Bioinformatics , vol.23 , Issue.4 , pp. 421-426
    • Kowalsman, N.1    Eisenstein, M.2
  • 58
    • 5044235050 scopus 로고    scopus 로고
    • Ten thousand interactions for the molecular biologist
    • DOI 10.1038/nbt1018
    • Aloy P, Russell RB (2004) Ten thousand interactions for the molecular biologist. Nat Biotechnol 22: 1317-1321. (Pubitemid 39336787)
    • (2004) Nature Biotechnology , vol.22 , Issue.10 , pp. 1317-1321
    • Aloy, P.1    Russell, R.B.2
  • 59
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • DOI 10.1002/prot.10115
    • Halperin I, Ma B, Wolfson H, Nussinov R (2002) Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 47: 409-443. (Pubitemid 34614722)
    • (2002) Proteins: Structure, Function and Genetics , vol.47 , Issue.4 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 61
    • 54249117223 scopus 로고    scopus 로고
    • Targeting and tinkering with interaction networks
    • Russell RB, Aloy P (2008) Targeting and tinkering with interaction networks. Nat Chem Biol 4: 666-673.
    • (2008) Nat Chem Biol , vol.4 , pp. 666-673
    • Russell, R.B.1    Aloy, P.2
  • 62
    • 53349117774 scopus 로고    scopus 로고
    • High-quality binary protein interaction map of the yeast interactome network
    • Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322: 104-110.
    • (2008) Science , vol.322 , pp. 104-110
    • Yu, H.1    Braun, P.2    Yildirim, M.A.3    Lemmens, I.4    Venkatesan, K.5
  • 63
    • 33947712535 scopus 로고    scopus 로고
    • WI-PHI: A weighted yeast interactome enriched for direct physical interactions
    • DOI 10.1002/pmic.200600448
    • Kiemer L, Costa S, Ueffing M, Cesareni G (2007) WI-PHI: a weighted yeast interactome enriched for direct physical interactions. Proteomics 7: 932-943. (Pubitemid 46506740)
    • (2007) Proteomics , vol.7 , Issue.6 , pp. 932-943
    • Kiemer, L.1    Costa, S.2    Ueffing, M.3    Cesareni, G.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.