메뉴 건너뛰기




Volumn 107, Issue 24, 2010, Pages 10896-10901

Protein interface conservation across structure space

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SURFACE PROPERTY;

EID: 77954636479     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1005894107     Document Type: Article
Times cited : (138)

References (38)
  • 1
    • 34047202181 scopus 로고    scopus 로고
    • Deciphering protein-protein interactions. Part I. Experimental techniques and databases
    • Shoemaker BA, Panchenko AR (2007) Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLoS Comput Biol 3:e42.
    • (2007) PLoS Comput Biol , vol.3
    • Shoemaker, B.A.1    Panchenko, A.R.2
  • 2
    • 34247586171 scopus 로고    scopus 로고
    • Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners
    • Shoemaker BA, Panchenko AR (2007) Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput Biol 3:e43.
    • (2007) PLoS Comput Biol , vol.3
    • Shoemaker, B.A.1    Panchenko, A.R.2
  • 3
    • 33644873184 scopus 로고    scopus 로고
    • BioGRID: A general repository for interaction datasets
    • Stark C, et al. (2006) BioGRID: A general repository for interaction datasets. Nucl Acids Res 34:D535-D539.
    • (2006) Nucl Acids Res , vol.34
    • Stark, C.1
  • 4
    • 33846047770 scopus 로고    scopus 로고
    • IntAct - Open source resource for molecular interaction data
    • Kerrien S, et al. (2007) IntAct - open source resource for molecular interaction data. Nucl Acids Res 35:D561-565.
    • (2007) Nucl Acids Res , vol.35
    • Kerrien, S.1
  • 5
    • 0037832188 scopus 로고    scopus 로고
    • Computational methods of analysis of protein-protein interactions
    • Salwinski L, Eisenberg D (2003) Computational methods of analysis of protein-protein interactions. Curr Opin Struct Biol 13:377-382.
    • (2003) Curr Opin Struct Biol , vol.13 , pp. 377-382
    • Salwinski, L.1    Eisenberg, D.2
  • 6
    • 27644576841 scopus 로고    scopus 로고
    • High-throughput two-hybrid analysis. The promise and the peril
    • Fields S (2005) High-throughput two-hybrid analysis. The promise and the peril. FEBS J 272:5391-5399.
    • (2005) FEBS J , vol.272 , pp. 5391-5399
    • Fields, S.1
  • 8
    • 12144290243 scopus 로고    scopus 로고
    • Structure-based assembly of protein complexes in yeast
    • Aloy P, et al. (2004) Structure-based assembly of protein complexes in yeast. Science 303:2026-2029.
    • (2004) Science , vol.303 , pp. 2026-2029
    • Aloy, P.1
  • 10
    • 0037110589 scopus 로고    scopus 로고
    • Multiprospector: An algorithm for the prediction of protein-protein interactions by multimeric threading
    • DOI 10.1002/prot.10222
    • Lu L, Lu H, Skolnick J (2002) MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 49:350-364. (Pubitemid 35231471)
    • (2002) Proteins: Structure, Function and Genetics , vol.49 , Issue.3 , pp. 350-364
    • Lu, L.1    Lu, H.2    Skolnick, J.3
  • 11
    • 70350465128 scopus 로고    scopus 로고
    • Structural relationships among proteins with different global topologies and their implications for function annotation strategies
    • Petrey D, Fischer M, Honig B (2009) Structural relationships among proteins with different global topologies and their implications for function annotation strategies. Proc Natl Acad Sci USA 106:17377-17382.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 17377-17382
    • Petrey, D.1    Fischer, M.2    Honig, B.3
  • 12
    • 0036307754 scopus 로고    scopus 로고
    • The geometry of domain combination in proteins
    • Bashton M, Chothia C (2002) The geometry of domain combination in proteins. J Mol Biol 315:927-939.
    • (2002) J Mol Biol , vol.315 , pp. 927-939
    • Bashton, M.1    Chothia, C.2
  • 13
    • 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
    • 12144281353 scopus 로고    scopus 로고
    • Conservation of orientation and sequence in protein domain-domain interactions
    • DOI 10.1016/j.jmb.2004.11.011, PII S0022283604014378
    • Littler SJ, Hubbard SJ (2005) Conservation of orientation and sequence in protein domain-domain interactions. J Mol Biol 345:1265-1279. (Pubitemid 40103507)
    • (2005) Journal of Molecular Biology , vol.345 , Issue.5 , pp. 1265-1279
    • Littler, S.J.1    Hubbard, S.J.2
  • 15
    • 24344441167 scopus 로고    scopus 로고
    • Localization of protein-binding sites within families of proteins
    • DOI 10.1110/ps.051571905
    • Korkin D, Davis FP, Sali A (2005) Localization of protein-binding sites within families of proteins. Protein Sci 14:2350-2360. (Pubitemid 41252804)
    • (2005) Protein Science , vol.14 , Issue.9 , pp. 2350-2360
    • Korkin, D.1    Davis, F.P.2    Sali, A.3
  • 16
    • 33749337098 scopus 로고    scopus 로고
    • The many faces of protein-protein interactions: A compendium of interface geometry
    • Kim WK, Henschel A, Winter C, Schroeder M (2006) The many faces of protein-protein interactions: A compendium of interface geometry. PLoS Comput Biol 2:e124.
    • (2006) PLoS Comput Biol , vol.2
    • Kim, W.K.1    Henschel, A.2    Winter, C.3    Schroeder, M.4
  • 17
    • 28644448657 scopus 로고    scopus 로고
    • Survey of the geometric association of domain-domain interfaces
    • Kim WK, Ison JC (2005) Survey of the geometric association of domain-domain interfaces. Proteins 61:1075-1088.
    • (2005) Proteins , vol.61 , pp. 1075-1088
    • Kim, W.K.1    Ison, J.C.2
  • 18
    • 33646475098 scopus 로고    scopus 로고
    • Divergence of interdomain geometry in two-domain proteins
    • Han JH, Kerrison N, Chothia C, Teichmann SA (2006) Divergence of interdomain geometry in two-domain proteins. Structure 14:935-945.
    • (2006) Structure , vol.14 , pp. 935-945
    • Han, J.H.1    Kerrison, N.2    Chothia, C.3    Teichmann, S.A.4
  • 19
    • 31344459575 scopus 로고    scopus 로고
    • Finding biologically relevant protein domain interactions: Conserved binding mode analysis
    • Shoemaker BA, Panchenko AR, Bryant SH (2006) Finding biologically relevant protein domain interactions: conserved binding mode analysis. Protein Sci 15:352-361.
    • (2006) Protein Sci , vol.15 , pp. 352-361
    • Shoemaker, B.A.1    Panchenko, A.R.2    Bryant, S.H.3
  • 20
    • 33751088850 scopus 로고    scopus 로고
    • Biological units and their effect upon the properties and prediction of protein-protein interactions
    • Jefferson ER, Walsh TP, Barton GJ (2006) Biological units and their effect upon the properties and prediction of protein-protein interactions. J Mol Biol 364:1118-1129.
    • (2006) J Mol Biol , vol.364 , pp. 1118-1129
    • Jefferson, E.R.1    Walsh, T.P.2    Barton, G.J.3
  • 21
    • 0029988383 scopus 로고    scopus 로고
    • Protein-protein interfaces: Architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences
    • Tsai CJ, Lin SL, Wolfson HJ, Nussinov R (1996) Protein-protein interfaces: Architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences. Crit Rev Biochem Mol Biol 31:127-152.
    • (1996) Crit Rev Biochem Mol Biol , vol.31 , pp. 127-152
    • Tsai, C.J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 22
    • 17144366191 scopus 로고    scopus 로고
    • Favorable scaffolds: Proteins with different sequence, structure and function may associate in similar ways
    • Keskin O, Nussinov R (2005) Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways. Protein Eng Des Sel 18:11-24.
    • (2005) Protein Eng Des Sel , vol.18 , pp. 11-24
    • Keskin, O.1    Nussinov, R.2
  • 23
    • 0032475963 scopus 로고    scopus 로고
    • Supersites within superfolds. Binding site similarity in the absence of homology
    • Russell RB, Sasieni PD, Sternberg MJ (1998) Supersites within superfolds. Binding site similarity in the absence of homology. J Mol Biol 282:903-918.
    • (1998) J Mol Biol , vol.282 , pp. 903-918
    • Russell, R.B.1    Sasieni, P.D.2    Sternberg, M.J.3
  • 24
    • 38349100452 scopus 로고    scopus 로고
    • A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
    • Brylinski M, Skolnick J (2008) A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci USA 105:129-134.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 129-134
    • Brylinski, M.1    Skolnick, J.2
  • 25
    • 23144451857 scopus 로고    scopus 로고
    • Fragnostic: Walking through protein structure space
    • Friedberg I, Godzik A (2005) Fragnostic: Walking through protein structure space. Nucl Acids Res 33:W249-251.
    • (2005) Nucl Acids Res , vol.33
    • Friedberg, I.1    Godzik, A.2
  • 27
    • 0346122798 scopus 로고    scopus 로고
    • GRASP2: Visualization, Surface Properties, and Electrostatics of Macromolecular Structures and Sequences
    • Petrey D, Honig B (2003) GRASP2: Visualization, Surface Properties, and Electrostatics of Macromolecular Structures and Sequences. Methods Enzymol 374:492-509.
    • (2003) Methods Enzymol , vol.374 , pp. 492-509
    • Petrey, D.1    Honig, B.2
  • 28
    • 0034682881 scopus 로고    scopus 로고
    • An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance
    • Yang AS, Honig B (2000) An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance. J Mol Biol 301:665-678.
    • (2000) J Mol Biol , vol.301 , pp. 665-678
    • Yang, A.S.1    Honig, B.2
  • 29
    • 34447286908 scopus 로고    scopus 로고
    • The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007
    • Janin J, Wodak S (2007) The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007. Structure 15:755-759.
    • (2007) Structure , vol.15 , pp. 755-759
    • Janin, J.1    Wodak, S.2
  • 30
    • 24344484686 scopus 로고    scopus 로고
    • Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data
    • Chen HL, Zhou HX (2005) Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data. Proteins 61:21-35.
    • (2005) Proteins , vol.61 , pp. 21-35
    • Chen, H.L.1    Zhou, H.X.2
  • 31
    • 33747150197 scopus 로고    scopus 로고
    • Protein binding site prediction using an empirical scoring function
    • DOI 10.1093/nar/gkl454
    • Liang S, Zhang C, Liu S, Zhou Y (2006) Protein binding site prediction using an empirical scoring function. Nucl Acids Res 34:3698-3707. (Pubitemid 44400419)
    • (2006) Nucleic Acids Research , vol.34 , Issue.13 , pp. 3698-3707
    • Liang, S.1    Zhang, C.2    Liu, S.3    Zhou, Y.4
  • 32
    • 1842526090 scopus 로고    scopus 로고
    • ProMate: A structure based prediction program to identify the location of protein-protein binding sites
    • DOI 10.1016/j.jmb.2004.02.040, PII S0022283604002086
    • Neuvirth H, Raz R, Schreiber G (2004) ProMate: A structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 338:181-199. (Pubitemid 38429796)
    • (2004) Journal of Molecular Biology , vol.338 , Issue.1 , pp. 181-199
    • Neuvirth, H.1    Raz, R.2    Schreiber, G.3
  • 33
    • 34548767667 scopus 로고    scopus 로고
    • Interaction-site prediction for protein complexes: A critical assessment
    • DOI 10.1093/bioinformatics/btm323
    • Zhou HX, Qin S (2007) Interaction-site prediction for protein complexes: A critical assessment. Bioinformatics 23:2203-2209. (Pubitemid 47423856)
    • (2007) Bioinformatics , vol.23 , Issue.17 , pp. 2203-2209
    • Zhou, H.-X.1    Qin, S.2
  • 34
    • 23444459516 scopus 로고    scopus 로고
    • Connecting the protein structure universe by using sparse recurring fragments
    • DOI 10.1016/j.str.2005.05.009, PII S0969212605002169
    • Friedberg I, Godzik A (2005) Connecting the protein structure universe by using sparse recurring fragments. Structure 13:1213-1224. (Pubitemid 41111488)
    • (2005) Structure , vol.13 , Issue.8 , pp. 1213-1224
    • Friedberg, I.1    Godzik, A.2
  • 35
    • 0032169688 scopus 로고    scopus 로고
    • PQS: A protein quaternary structure file server
    • DOI 10.1016/S0968-0004(98)01253-5, PII S0968000498012535
    • Henrick K, Thornton JM (1998) PQS: A protein quaternary structure file server. Trends Biochem Sci 23:358-361. (Pubitemid 28461869)
    • (1998) Trends in Biochemical Sciences , vol.23 , Issue.9 , pp. 358-361
    • Henrick, K.1    Thornton, J.M.2
  • 36
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li WZ, Godzik A (2006) Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.Z.1    Godzik, A.2
  • 37
    • 38549153238 scopus 로고    scopus 로고
    • Data growth and its impact on the SCOP database: New developments
    • Andreeva A, et al. (2008) Data growth and its impact on the SCOP database: New developments. Nucl Acids Res 36:D419-425.
    • (2008) Nucl Acids Res , vol.36
    • Andreeva, A.1
  • 38
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • DOI 10.1006/jmbi.1993.1626
    • Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779-815. (Pubitemid 24007801)
    • (1993) Journal of Molecular Biology , vol.234 , Issue.3 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.