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Volumn 3, Issue 7, 2007, Pages 1169-1176

Protein-protein interaction hotspots carved into sequences

Author keywords

[No Author keywords available]

Indexed keywords

FORECASTING;

EID: 34547573955     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030119     Document Type: Article
Times cited : (231)

References (46)
  • 1
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
    • Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
    • (2000) Nature , vol.403 , pp. 623-627
    • Uetz, P.1    Giot, L.2    Cagney, G.3    Mansfield, T.A.4    Judson, R.S.5
  • 2
    • 0037050004 scopus 로고    scopus 로고
    • Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
    • Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183.
    • (2002) Nature , vol.415 , pp. 180-183
    • Ho, Y.1    Gruhler, A.2    Heilbut, A.3    Bader, G.D.4    Moore, L.5
  • 3
    • 0037050026 scopus 로고    scopus 로고
    • Functional organization of the yeast proteome by systematic analysis of protein complexes
    • Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
    • (2002) Nature , vol.415 , pp. 141-147
    • Gavin, A.C.1    Bosche, M.2    Krause, R.3    Grandi, P.4    Marzioch, M.5
  • 4
    • 0345600247 scopus 로고    scopus 로고
    • A protein interaction map of Drosophila melanogaster
    • Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, et al. (2003) A protein interaction map of Drosophila melanogaster. Science 302: 1727-1736.
    • (2003) Science , vol.302 , pp. 1727-1736
    • Giot, L.1    Bader, J.S.2    Brouwer, C.3    Chaudhuri, A.4    Kuang, B.5
  • 5
    • 9144264169 scopus 로고    scopus 로고
    • A map of the interactome network of the metazoan C. elegans
    • Li S, Armstrong CM, Bertin N, Ge H, Milstein S, et al. (2004) A map of the interactome network of the metazoan C. elegans. Science 303: 540-543.
    • (2004) Science , vol.303 , pp. 540-543
    • Li, S.1    Armstrong, C.M.2    Bertin, N.3    Ge, H.4    Milstein, S.5
  • 6
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • Bogan AA, Thorn KS (1998) Anatomy of hot spots in protein interfaces. J Mol Biol 280: 1-9.
    • (1998) J Mol Biol , vol.280 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 7
    • 0036469060 scopus 로고    scopus 로고
    • Unraveling hot spots in binding interfaces: Progress and challenges
    • DeLano WL (2002) Unraveling hot spots in binding interfaces: Progress and challenges. Curr Opin Struct Biol 12: 14-20.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 14-20
    • DeLano, W.L.1
  • 8
    • 0032543307 scopus 로고    scopus 로고
    • Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody
    • Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J, et al. (1998) Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature 393: 648-659.
    • (1998) Nature , vol.393 , pp. 648-659
    • Kwong, P.D.1    Wyatt, R.2    Robinson, J.3    Sweet, R.W.4    Sodroski, J.5
  • 9
    • 0026350498 scopus 로고
    • Systematic mutational analyses of protein-protein interfaces
    • Wells JA (1991) Systematic mutational analyses of protein-protein interfaces. Methods Enzymol 202: 390-411.
    • (1991) Methods Enzymol , vol.202 , pp. 390-411
    • Wells, J.A.1
  • 11
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormone-receptor interface
    • Clackson T, Wells JA (1995) A hot spot of binding energy in a hormone-receptor interface. Science 267: 383-386.
    • (1995) Science , vol.267 , pp. 383-386
    • Clackson, T.1    Wells, J.A.2
  • 12
    • 0035066602 scopus 로고    scopus 로고
    • ASEdb: A database of alanine mutations and their effects on the free energy of binding in protein interactions
    • Thorn KS, Bogan AA (2001) ASEdb: A database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics 17: 284-285.
    • (2001) Bioinformatics , vol.17 , pp. 284-285
    • Thorn, K.S.1    Bogan, A.A.2
  • 13
    • 0026598960 scopus 로고
    • Human growth hormone and extracellular domain of its receptor: Crystal structure of the complex
    • de Vos AM, Ultsch M, Kossiakoff AA (1992) Human growth hormone and extracellular domain of its receptor: Crystal structure of the complex. Science 255: 306-312.
    • (1992) Science , vol.255 , pp. 306-312
    • de Vos, A.M.1    Ultsch, M.2    Kossiakoff, A.A.3
  • 14
    • 0030322783 scopus 로고    scopus 로고
    • Double-mutant cycles: A powerful tool for analyzing protein structure and function
    • Horovitz A (1996) Double-mutant cycles: A powerful tool for analyzing protein structure and function. Fold Des 1: R121-R126.
    • (1996) Fold Des , vol.1
    • Horovitz, A.1
  • 15
    • 0033548664 scopus 로고    scopus 로고
    • Structural response to mutation at a protein-protein interface
    • Vaughan CK, Buckle AM, Fersht AR (1999) Structural response to mutation at a protein-protein interface. J Mol Biol 286: 1487-1506.
    • (1999) J Mol Biol , vol.286 , pp. 1487-1506
    • Vaughan, C.K.1    Buckle, A.M.2    Fersht, A.R.3
  • 17
    • 0037093645 scopus 로고    scopus 로고
    • Dissecting protein-protein recognition sites
    • Chakrabarti P, Janin J (2002) Dissecting protein-protein recognition sites. Proteins 47: 334-343.
    • (2002) Proteins , vol.47 , pp. 334-343
    • Chakrabarti, P.1    Janin, J.2
  • 18
    • 31944439550 scopus 로고    scopus 로고
    • Exploiting sequence and structure homologs to identify protein-protein binding sites
    • Chung JL, Wang W, Bourne PE (2006) Exploiting sequence and structure homologs to identify protein-protein binding sites. Proteins 62: 630-640.
    • (2006) Proteins , vol.62 , pp. 630-640
    • Chung, J.L.1    Wang, W.2    Bourne, P.E.3
  • 19
    • 0036122073 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites in heterocomplexes with neural networks
    • Fariselli P, Pazos F, Valencia A, Casadio R (2002) Prediction of protein-protein interaction sites in heterocomplexes with neural networks. Eur J Biochem 269: 1356-1361.
    • (2002) Eur J Biochem , vol.269 , pp. 1356-1361
    • Fariselli, P.1    Pazos, F.2    Valencia, A.3    Casadio, R.4
  • 20
    • 1542390499 scopus 로고    scopus 로고
    • Identification of protein-protein interaction sites from docking energy landscapes
    • Fernandez-Recio J, Totrov M, Abagyan R (2004) Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 335: 843-865.
    • (2004) J Mol Biol , vol.335 , pp. 843-865
    • Fernandez-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 21
    • 10844235653 scopus 로고    scopus 로고
    • Optimal docking area: A new method for predicting protein-protein interaction sites
    • Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R (2005) Optimal docking area: A new method for predicting protein-protein interaction sites. Proteins 58: 134-143.
    • (2005) Proteins , vol.58 , pp. 134-143
    • Fernandez-Recio, J.1    Totrov, M.2    Skorodumov, C.3    Abagyan, R.4
  • 22
    • 0034730415 scopus 로고    scopus 로고
    • A fast method to predict protein interaction sites from sequences
    • Gallet X, Charloteaux B, Thomas A, Brasseur R (2000) A fast method to predict protein interaction sites from sequences. J Mol Biol 302: 917-926.
    • (2000) J Mol Biol , vol.302 , pp. 917-926
    • Gallet, X.1    Charloteaux, B.2    Thomas, A.3    Brasseur, R.4
  • 23
    • 0035342450 scopus 로고    scopus 로고
    • Residue frequencies and pairing preferences at protein-protein interfaces
    • Glaser F, Steinberg DM, Vakser IA, Ben-Tal N (2001) Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 43: 89-102.
    • (2001) Proteins , vol.43 , pp. 89-102
    • Glaser, F.1    Steinberg, D.M.2    Vakser, I.A.3    Ben-Tal, N.4
  • 24
    • 0031565725 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using patch analysis
    • Jones S, Thornton JM (1997) Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 272: 133-143.
    • (1997) J Mol Biol , vol.272 , pp. 133-143
    • Jones, S.1    Thornton, J.M.2
  • 25
    • 1842765629 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using support vector machines
    • Koike A, Takagi T (2004) Prediction of protein-protein interaction sites using support vector machines. Protein Eng Des Sel 17: 165-173.
    • (2004) Protein Eng Des Sel , vol.17 , pp. 165-173
    • Koike, A.1    Takagi, T.2
  • 26
    • 1842526090 scopus 로고    scopus 로고
    • ProMate: A structure based prediction program to identify the location of protein-protein binding sites
    • 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.
    • (2004) J Mol Biol , vol.338 , pp. 181-199
    • Neuvirth, H.1    Raz, R.2    Schreiber, G.3
  • 27
    • 0037229456 scopus 로고    scopus 로고
    • Analysing six types of protein-protein interfaces
    • Ofran Y, Rost B (2003) Analysing six types of protein-protein interfaces. J Mol Biol 325: 377-387.
    • (2003) J Mol Biol , vol.325 , pp. 377-387
    • Ofran, Y.1    Rost, B.2
  • 28
    • 33846662784 scopus 로고    scopus 로고
    • ISIS: Interaction Sites Identified from Sequence
    • Ofran Y, Rost B (2007) ISIS: Interaction Sites Identified from Sequence. Bioinformatics 23: e13-e16.
    • (2007) Bioinformatics , vol.23
    • Ofran, Y.1    Rost, B.2
  • 29
    • 0038356582 scopus 로고    scopus 로고
    • Predicted protein-protein interaction sites from local sequence information
    • Ofran Y, Rost B (2003) Predicted protein-protein interaction sites from local sequence information. FEBS Lett 544: 236-239.
    • (2003) FEBS Lett , vol.544 , pp. 236-239
    • Ofran, Y.1    Rost, B.2
  • 30
    • 19544369864 scopus 로고    scopus 로고
    • An evolution based classifier for prediction of protein interfaces without using protein structures
    • Res I, Mihalek I, Lichtarge O (2005) An evolution based classifier for prediction of protein interfaces without using protein structures. Bioinformatics 21: 2496-2501.
    • (2005) Bioinformatics , vol.21 , pp. 2496-2501
    • Res, I.1    Mihalek, I.2    Lichtarge, O.3
  • 31
    • 30644470508 scopus 로고    scopus 로고
    • Predicting protein interaction sites from residue spatial sequence profile and evolution rate
    • Wang B, Chen P, Huang DS, Li JJ, Lok TM, et al. (2005) Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett 580: 380-384.
    • (2005) FEBS Lett , vol.580 , pp. 380-384
    • Wang, B.1    Chen, P.2    Huang, D.S.3    Li, J.J.4    Lok, T.M.5
  • 32
    • 1842861590 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions: The CAPRI experiment, its evaluation and implications
    • Wodak SJ, Mendez R (2004) Prediction of protein-protein interactions: The CAPRI experiment, its evaluation and implications. Curr Opin Struct Biol 14: 242-249.
    • (2004) Curr Opin Struct Biol , vol.14 , pp. 242-249
    • Wodak, S.J.1    Mendez, R.2
  • 34
    • 0030064382 scopus 로고    scopus 로고
    • Spatial localization of the K+ channel selectivity filter by mutant cycle-based structure analysis
    • Ranganathan R, Lewis JH, MacKinnon R (1996) Spatial localization of the K+ channel selectivity filter by mutant cycle-based structure analysis. Neuron 16: 131-139.
    • (1996) Neuron , vol.16 , pp. 131-139
    • Ranganathan, R.1    Lewis, J.H.2    MacKinnon, R.3
  • 35
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge O, Bourne HR, Cohen FE (1996) An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 257: 342-358.
    • (1996) J Mol Biol , vol.257 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 36
    • 0019934717 scopus 로고
    • The helical hydrophobic moment: A measure of the amphiphilicity of a helix
    • Eisenberg D, Weiss RM, Terwilliger TC (1982) The helical hydrophobic moment: A measure of the amphiphilicity of a helix. Nature 299: 371-374.
    • (1982) Nature , vol.299 , pp. 371-374
    • Eisenberg, D.1    Weiss, R.M.2    Terwilliger, T.C.3
  • 37
    • 11844249426 scopus 로고    scopus 로고
    • Hot regions in protein-protein interactions: The organization and contribution of structurally conserved hot spot residues
    • Keskin O, Ma B, Nussinov R (2005) Hot regions in protein-protein interactions: The organization and contribution of structurally conserved hot spot residues. J Mol Biol 345: 1281-1294.
    • (2005) J Mol Biol , vol.345 , pp. 1281-1294
    • Keskin, O.1    Ma, B.2    Nussinov, R.3
  • 38
    • 2942553723 scopus 로고    scopus 로고
    • Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking
    • Halperin I, Wolfson H, Nussinov R (2004) Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. Structure 12: 1027-1038.
    • (2004) Structure , vol.12 , pp. 1027-1038
    • Halperin, I.1    Wolfson, H.2    Nussinov, R.3
  • 39
    • 3242879771 scopus 로고    scopus 로고
    • Computational alanine scanning of protein-protein interfaces
    • Kortemme T, Kim DE, Baker D (2004) Computational alanine scanning of protein-protein interfaces. Sci STKE 2004: pl2.
    • (2004) Sci STKE 2004: Pl2
    • Kortemme, T.1    Kim, D.E.2    Baker, D.3
  • 40
    • 0037195144 scopus 로고    scopus 로고
    • A simple physical model for binding energy hot spots in protein-protein complexes
    • Kortemme T, Baker D (2002) A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci U S A 99: 14116-14121.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 41
    • 0030801002 scopus 로고    scopus 로고
    • Gapped Blast and PSI-Blast: A new generation of protein database search programs
    • Altschul S, Madden T, Shaffer A, Zhang J, Zhang Z, et al. (1997) Gapped Blast and PSI-Blast: A new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.1    Madden, T.2    Shaffer, A.3    Zhang, J.4    Zhang, Z.5
  • 42
    • 10844291320 scopus 로고    scopus 로고
    • Prediction in 1D: Secondary structure, membrane helices, and accessibility
    • Bourne P, Weissig H, editors, Hoboken New Jersey, Wiley-Liss. 649 p
    • Rost B (2002) Prediction in 1D: Secondary structure, membrane helices, and accessibility. In: Bourne P, Weissig H, editors. Structural bioinformatics. Hoboken (New Jersey): Wiley-Liss. 649 p.
    • (2002) Structural bioinformatics
    • Rost, B.1
  • 43
    • 0037197902 scopus 로고    scopus 로고
    • Interrogating protein interaction networks through structural biology
    • Aloy P, Russell RB (2002) Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci 99: 5896-5901.
    • (2002) Proc Natl Acad Sci , vol.99 , pp. 5896-5901
    • Aloy, P.1    Russell, R.B.2
  • 44
    • 0036228122 scopus 로고    scopus 로고
    • Structural similarity to link sequence space: New potential superfamilies and implications for structural genomics
    • Aloy P, Oliva B, Querol E, Aviles FX, Russell RB (2002) Structural similarity to link sequence space: New potential superfamilies and implications for structural genomics. Protein Sci 11: 1101-1116.
    • (2002) Protein Sci , vol.11 , pp. 1101-1116
    • Aloy, P.1    Oliva, B.2    Querol, E.3    Aviles, F.X.4    Russell, R.B.5
  • 45
    • 0034459679 scopus 로고    scopus 로고
    • Evolutionary trace analysis of TGF-beta and related growth factors: Implications for site-directed mutagenesis
    • Innis CA, Shi J, Blundell TL (2000) Evolutionary trace analysis of TGF-beta and related growth factors: Implications for site-directed mutagenesis. Protein Eng 13: 839-847.
    • (2000) Protein Eng , vol.13 , pp. 839-847
    • Innis, C.A.1    Shi, J.2    Blundell, T.L.3
  • 46
    • 0029960050 scopus 로고    scopus 로고
    • The HSSP database of protein structure-sequence alignments
    • Schneider R, Sander C (1996) The HSSP database of protein structure-sequence alignments. Nucleic Acids Res 24: 201-205.
    • (1996) Nucleic Acids Res , vol.24 , pp. 201-205
    • Schneider, R.1    Sander, C.2


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