메뉴 건너뛰기




Volumn 9, Issue , 2008, Pages

Identification of hot-spot residues in protein-protein interactions by computational docking

Author keywords

[No Author keywords available]

Indexed keywords

3D STRUCTURE; COMPUTATIONAL APPROACH; COMPUTATIONAL DOCKINGS; POSITIVE PREDICTIVE VALUES; PROTEIN-PROTEIN BINDING; PROTEIN-PROTEIN INTERACTIONS; RIGID-BODY DOCKING; STRUCTURAL KNOWLEDGE;

EID: 55649090573     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-447     Document Type: Article
Times cited : (98)

References (36)
  • 1
    • 3142781225 scopus 로고    scopus 로고
    • Small-molecules inhibitors of protein-protein interactions: Progressing toward the dreams
    • 10.1038/nrd1343 15060526
    • Arkin MR Wells JA Small-molecules inhibitors of protein-protein interactions: Progressing toward the dreams Nat Rev Drug Discov 2004, 3:301-317. 10.1038/nrd1343 15060526
    • (2004) Nat Rev Drug Discov , vol.3 , pp. 301-317
    • Arkin, M.R.1    Wells, J.A.2
  • 2
    • 0037061646 scopus 로고    scopus 로고
    • Inhibition of protein-protein association by small molecules: Approaches and progress
    • 10.1021/jm010468s 11931608
    • Toogood PL Inhibition of protein-protein association by small molecules: approaches and progress J Med Chem 2002, 45:1543-1558. 10.1021/jm010468s 11931608
    • (2002) J Med Chem , vol.45 , pp. 1543-1558
    • Toogood, P.L.1
  • 3
    • 0036469060 scopus 로고    scopus 로고
    • Unraveling hot-spots in binding interfaces: Progress and challenges
    • 10.1016/S0959-440X(02)00283-X
    • DeLano WL Unraveling hot-spots in binding interfaces: Progress and challenges Curr Opin Struct Biol 2002, 12:14-20. 10.1016/ S0959-440X(02)00283-X 11839484
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 14-20
    • DeLano, W.L.1
  • 4
    • 33846094031 scopus 로고    scopus 로고
    • Computational identification of inhibitors of protein-protein interactions
    • 10.2174/156802607779318334 17266596
    • Zhong S Macias AT MacKerrell AD Computational identification of inhibitors of protein-protein interactions Curr Top Med Chem 2007, 7:63-82. 10.2174/156802607779318334 17266596
    • (2007) Curr Top Med Chem , vol.7 , pp. 63-82
    • Zhong, S.1    Macias, A.T.2    MacKerrell, A.D.3
  • 5
    • 34548779127 scopus 로고    scopus 로고
    • Hot spots-a review of the protein-protein interface determinant amino-acid residues
    • 10.1002/prot.21396 17546660
    • Moreira IS Fernandes PA Ramos MJ Hot spots-a review of the protein-protein interface determinant amino-acid residues Proteins 2007, 68:803-812. 10.1002/prot.21396 17546660
    • (2007) Proteins , vol.68 , pp. 803-812
    • Moreira, I.S.1    Fernandes, P.A.2    Ramos, M.J.3
  • 6
    • 0030028728 scopus 로고    scopus 로고
    • Principles of protein-protein interactions
    • 40170 8552589 10.1073/pnas.93.1.13
    • Jones S Thornton JM Principles of protein-protein interactions Proc Natl Acad Sci USA 1996, 93:13-20. 40170 8552589 10.1073/pnas.93.1.13
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 13-20
    • Jones, S.1    Thornton, J.M.2
  • 7
    • 0031565729 scopus 로고    scopus 로고
    • Analysis of protein-protein interaction sites using surface patches
    • 10.1006/jmbi.1997.1234 9299342
    • Jones S Thornton JM Analysis of protein-protein interaction sites using surface patches J Mol Biol 1997, 272:121-132. 10.1006/jmbi.1997.1234 9299342
    • (1997) J Mol Biol , vol.272 , pp. 121-132
    • Jones, S.1    Thornton, J.M.2
  • 8
    • 11844249426 scopus 로고    scopus 로고
    • Hot regions in protein-protein interactions: The organization and contribution of structurally conserved hot-spot residues
    • 10.1016/j.jmb.2004.10.077 15644221
    • Keskin O Ma B Nussinov R Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot-spot residues J Mol Biol 2005, 345:1281-1294. 10.1016/j.jmb.2004.10.077 15644221
    • (2005) J Mol Biol , vol.345 , pp. 1281-1294
    • Keskin, O.1    Ma, B.2    Nussinov, R.3
  • 9
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot-spots in protein interfaces
    • 10.1006/jmbi.1998.1843 9653027
    • Bogan AA Thorn KS Anatomy of hot-spots in protein interfaces J Mol Biol 1998, 280:1-9. 10.1006/jmbi.1998.1843 9653027
    • (1998) J Mol Biol , vol.280 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 10
    • 34547573955 scopus 로고    scopus 로고
    • Protein-protein interaction hotspots carved into sequences
    • 1914369 17630824 10.1371/journal.pcbi.0030119
    • Ofran Y Rost B Protein-protein interaction hotspots carved into sequences PLoS Comput Biol 2007, 3:e119. 1914369 17630824 10.1371/ journal.pcbi.0030119
    • (2007) PLoS Comput Biol , vol.3
    • Ofran, Y.1    Rost, B.2
  • 11
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • 10.1006/jmbi.1998.2439 9925793
    • Lo Conte L Chothia C Janin J The atomic structure of protein-protein recognition sites J Mol Biol 1999, 285:2177-2198. 10.1006/jmbi.1998.2439 9925793
    • (1999) J Mol Biol , vol.285 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 12
    • 0034213559 scopus 로고    scopus 로고
    • Conservation of polar residues as hot-spots at protein interfaces
    • 10.1002/(SICI)1097-0134(20000601)39:4<331::AID-PROT60<3.0.CO;2-A 10813815
    • Hu Z Ma B Wolfson H Nussinov R Conservation of polar residues as hot-spots at protein interfaces Proteins 2000, 39:331-342. 10.1002/ (SICI)1097-0134(20000601)39:4<331::AID-PROT60<3.0.CO;2-A 10813815
    • (2000) Proteins , vol.39 , pp. 331-342
    • Hu, Z.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 13
    • 0037609791 scopus 로고    scopus 로고
    • Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces
    • 156276 12730379 10.1073/pnas.1030237100
    • Ma B Elkayam T Wolfson H Nussinov R Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces Proc Natl Acad Sci USA 2003, 100:5772-5777. 156276 12730379 10.1073/pnas.1030237100
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 5772-5777
    • Ma, B.1    Elkayam, T.2    Wolfson, H.3    Nussinov, R.4
  • 14
    • 0037195144 scopus 로고    scopus 로고
    • A simple physical model for binding energy hot-spots in protein-protein complexes
    • 137846 12381794 10.1073/pnas.202485799
    • Kortemme T Baker D A simple physical model for binding energy hot-spots in protein-protein complexes Proc Natl Acad Sci 2002, 99:14116-14121. 137846 12381794 10.1073/pnas.202485799
    • (2002) Proc Natl Acad Sci , vol.99 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 15
    • 3242879771 scopus 로고    scopus 로고
    • Computational alanine scanning of protein-protein interfaces
    • Kortemme T Kim DE Baker D Computational alanine scanning of protein-protein interfaces Sci STKE 2004:12.
    • (2004) Sci STKE , pp. 12
    • Kortemme, T.1    Kim, D.E.2    Baker, D.3
  • 16
    • 33646166928 scopus 로고    scopus 로고
    • Probing the effect of point mutations at protein-protein interfaces with free energy calculations
    • 1367050 16272444 10.1529/biophysj.105.073239
    • Almlöf M Aqvist J Smalås AO Brandsdal BO Probing the effect of point mutations at protein-protein interfaces with free energy calculations Biophys J 2006, 90:433-442. 1367050 16272444 10.1529/ biophysj.105.073239
    • (2006) Biophys J , vol.90 , pp. 433-442
    • Almlöf, M.1    Aqvist, J.2    Smalås, A.O.3    Brandsdal, B.O.4
  • 17
    • 33847650393 scopus 로고    scopus 로고
    • Computational alanine scanning mutagenesis - An improved methodological approach
    • 10.1002/jcc.20566
    • Moreira IS Fernandes PA Ramos MJ Computational alanine scanning mutagenesis - An improved methodological approach Nat J Comput Chem 2007, 28:644-654. 10.1002/jcc.20566
    • (2007) Nat J Comput Chem , vol.28 , pp. 644-654
    • Moreira, I.S.1    Fernandes, P.A.2    Ramos, M.J.3
  • 18
    • 34548764386 scopus 로고    scopus 로고
    • An automated decision-tree apporach to predicting protein interaction hot spots
    • 10.1002/prot.21474 17554779
    • Darnell SJ Page D Mitchell JC An automated decision-tree apporach to predicting protein interaction hot spots Proteins 2007, 68:813-823. 10.1002/prot.21474 17554779
    • (2007) Proteins , vol.68 , pp. 813-823
    • Darnell, S.J.1    Page, D.2    Mitchell, J.C.3
  • 19
    • 1542390499 scopus 로고    scopus 로고
    • Identification of protein-protein interaction sites from docking energy landscapes
    • 10.1016/j.jmb.2003.10.069 14687579
    • Fernández-Recio J Totrov M Abagyan R Identification of protein-protein interaction sites from docking energy landscapes J Mol Biol 2004, 335:843-865. 10.1016/j.jmb.2003.10.069 14687579
    • (2004) J Mol Biol , vol.335 , pp. 843-865
    • Fernández-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 20
  • 21
    • 34250882254 scopus 로고    scopus 로고
    • PyDock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking
    • 10.1002/prot.21419 17444519
    • Man-Kuang Cheng T Blundell TL Fernández-Recio J PyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking Proteins 2007, 68:503-515 10.1002/ prot.21419 17444519
    • (2007) Proteins , vol.68 , pp. 503-515
    • Man-Kuang Cheng, T.1    Blundell, T.L.2    Fernández-Recio, J.3
  • 22
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • 10.1006/jmbi.1997.1203 9299341
    • Gabb HA Jackson RM Sternberg MJ Modelling protein docking using shape complementarity, electrostatics and biochemical information J Mol Biol 1997, 272:106-120 10.1006/jmbi.1997.1203 9299341
    • (1997) J Mol Biol , vol.272 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.3
  • 23
    • 0038185277 scopus 로고    scopus 로고
    • A novel shape complementarity scoring function for protein-protein docking
    • 10.1002/prot.10334 12696051
    • Chen R Weng Z A novel shape complementarity scoring function for protein-protein docking Proteins 2003, 51:397-408 10.1002/prot.10334 12696051
    • (2003) Proteins , vol.51 , pp. 397-408
    • Chen, R.1    Weng, Z.2
  • 24
    • 0032906377 scopus 로고    scopus 로고
    • Mechanism of folding and assembly of a small tetrameric protein domain from tumor suppressor p53
    • 10.1038/5880 10048932
    • Mateu MG Pino MMSD Fresht AR Mechanism of folding and assembly of a small tetrameric protein domain from tumor suppressor p53 Nat Struct Biol 1999, 6:191-198. 10.1038/5880 10048932
    • (1999) Nat Struct Biol , vol.6 , pp. 191-198
    • Mateu, M.G.1    Pino, M.M.S.D.2    Fresht, A.R.3
  • 25
    • 10844235653 scopus 로고    scopus 로고
    • Optimal docking area: A new method for predicting protein-protein interaction sites
    • 10.1002/prot.20285 15495260
    • Fernández-Recio J Totrov M Skorodumov C Abagyan R Optimal docking area: A new method for predicting protein-protein interaction sites Proteins 2005, 58:134-143. 10.1002/prot.20285 15495260
    • (2005) Proteins , vol.58 , pp. 134-143
    • Fernández-Recio, J.1    Totrov, M.2    Skorodumov, C.3    Abagyan, R.4
  • 26
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
    • 10.1016/S0022-2836(02)00442-4 12079393
    • Guerois R Nielsen JE Serrano L Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations J Mol Biol 2002, 320:369-387. 10.1016/S0022-2836(02)00442-4 12079393
    • (2002) J Mol Biol , vol.320 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 28
    • 55649111264 scopus 로고    scopus 로고
    • Identification of hot spot residues at protein-protein interface
    • 1891667 17597870
    • Li L Zhao B Cui Z Gan J Sakharkar MK Kangueane P Identification of hot spot residues at protein-protein interface Bioinformation 2006, 1:121-126. 1891667 17597870
    • (2006) Bioinformation , vol.1 , pp. 121-126
    • Li, L.1    Zhao, B.2    Cui, Z.3    Gan, J.4    Sakharkar, M.K.5    Kangueane, P.6
  • 29
    • 1842526090 scopus 로고    scopus 로고
    • ProMate: A structure based prediction program to identify the location of protein-protein binding sites
    • 10.1016/j.jmb.2004.02.040 15050833
    • Neuvirth H Raz R Schreiber G ProMate: A structure based prediction program to identify the location of protein-protein binding sites J Mol Biol 2004, 338:181-199. 10.1016/j.jmb.2004.02.040 15050833
    • (2004) J Mol Biol , vol.338 , pp. 181-199
    • Neuvirth, H.1    Raz, R.2    Schreiber, G.3
  • 30
  • 31
    • 0031558771 scopus 로고    scopus 로고
    • Neutralizing epitopes on the extracellular interferon gamma receptor (IFNgammaR) alpha-chain characterized by homolog scanning mutagenesis and X-ray crystal structure of the A6 fab-IFNgammaR1-108 complex
    • 9367779
    • Sogabe S Stuart F Henke C Bridges A Williams G Birch A Winkler FK Robinson JA Neutralizing epitopes on the extracellular interferon gamma receptor (IFNgammaR) alpha-chain characterized by homolog scanning mutagenesis and X-ray crystal structure of the A6 fab-IFNgammaR1-108 complex Nat J Mol Biol 1997, 273:882-897. 9367779
    • (1997) Nat J Mol Biol , vol.273 , pp. 882-897
    • Sogabe, S.1    Stuart, F.2    Henke, C.3    Bridges, A.4    Williams, G.5    Birch, A.6    Winkler, F.K.7    Robinson, J.A.8
  • 32
    • 0035794194 scopus 로고    scopus 로고
    • High resolution mapping of the binding site on human IgG1 for Fc gamma RI, Fc gamma RII, Fc gamma RIII, and FcRn and design of IgG1 variants with improved binding to the Fc gamma R
    • 10.1074/jbc.M009483200 11096108
    • Shields RL Namenuk AK Hong K Meng YG Rae J Briggs J Xie D Lai J Stadlen A Li B Fox JA Presta LG High resolution mapping of the binding site on human IgG1 for Fc gamma RI, Fc gamma RII, Fc gamma RIII, and FcRn and design of IgG1 variants with improved binding to the Fc gamma R J Biol Chem 2001, 276:6591-6604. 10.1074/jbc.M009483200 11096108
    • (2001) J Biol Chem , vol.276 , pp. 6591-6604
    • Shields, R.L.1    Namenuk, A.K.2    Hong, K.3    Meng, Y.G.4    Rae, J.5    Briggs, J.6    Xie, D.7    Lai, J.8    Stadlen, A.9    Li, B.10    Fox, J.A.11    Presta, L.G.12
  • 34
    • 0035066602 scopus 로고    scopus 로고
    • ASEdb: A database of alanine mutations and their effects on the free energy of binding in protein interactions
    • 10.1093/bioinformatics/17.3.284 11294795
    • Thorn KS Bogan AA ASEdb: A database of alanine mutations and their effects on the free energy of binding in protein interactions Bioinformatics 2001, 17:284-285. 10.1093/bioinformatics/17.3.284 11294795
    • (2001) Bioinformatics , vol.17 , pp. 284-285
    • Thorn, K.S.1    Bogan, A.A.2
  • 35
    • 84886762262 scopus 로고    scopus 로고
    • MODBASE web server http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi
    • MODBASE Web Server


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.