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Volumn 22, Issue 8, 2013, Pages 1060-1070

A compound-based computational approach for the accurate determination of hot spots

Author keywords

Activin receptor; Activin signal pathway and nodal signal pathway; Cripto I; Hot spot; Hot spot prediction; Protein ligand docking; Protein protein docking; Protein protein interaction; Scoring function

Indexed keywords

ACTIVIN RECEPTOR; ALANINE; ALANTOLACTONE;

EID: 84881285169     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2296     Document Type: Article
Times cited : (6)

References (41)
  • 1
    • 33750303565 scopus 로고    scopus 로고
    • Hot-spot mimicry of a cytokine receptor by a small molecule
    • Thanos CD, DeLano WL, Wells JA (2006) Hot-spot mimicry of a cytokine receptor by a small molecule. Proc Nat Acad Sci 103:15422-15427.
    • (2006) Proc Nat Acad Sci , vol.103 , pp. 15422-15427
    • Thanos, C.D.1    Delano, W.L.2    Wells, J.A.3
  • 4
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormone-receptor interface
    • Clackson T, Wells J (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.2
  • 5
    • 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
  • 6
    • 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 Nat Acad Sci 99:14116-14121.
    • (2002) Proc Nat Acad Sci , vol.99 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 7
    • 33847650393 scopus 로고    scopus 로고
    • Computational alanine scanning mutagenesis-an improved methodological approach
    • Moreira J, Fernandez-Recio IS, Ramos MJ (2007) Computational alanine scanning mutagenesis-an improved methodological approach. Nat J Comput Chem 28: 644-654.
    • (2007) Nat J Comput Chem , vol.28 , pp. 644-654
    • Moreira, J.1    Fernandez-Recio, I.S.2    Ramos, M.J.3
  • 8
    • 55649090573 scopus 로고    scopus 로고
    • Identification of hot-spot residues in protein-protein interactions by computational docking
    • Grosdidier S, Fernandez-Recio J (2008) Identification of hot-spot residues in protein-protein interactions by computational docking. BMC Bioinformatics 9:447-460.
    • (2008) BMC Bioinformatics , vol.9 , pp. 447-460
    • Grosdidier, S.1    Fernandez-Recio, J.2
  • 9
    • 77954304081 scopus 로고    scopus 로고
    • Drugscore PPI webserver: Fast and accurate in silico alanine scanning for scoring protein-protein interactions
    • Krger DM, Gohlke H (2010) Drugscore PPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions. Nucl Acids Res 38(Suppl 2):W480-W486.
    • (2010) Nucl Acids Res , vol.38 , Issue.SUPPL. 2
    • Krger, D.M.1    Gohlke, H.2
  • 10
    • 79953060278 scopus 로고    scopus 로고
    • Context-based identification of protein-protein interfaces and hot-spot residues
    • Geppert T, Hoy B, Wessler S, Schneider G (2011) Context-based identification of protein-protein interfaces and hot-spot residues. Chem Biol 18:344-353.
    • (2011) Chem Biol , vol.18 , pp. 344-353
    • Geppert, T.1    Hoy, B.2    Wessler, S.3    Schneider, G.4
  • 11
    • 0037609791 scopus 로고    scopus 로고
    • Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces
    • Ma B, Elkayam T, Wolfson H, Nussinov R (2003) Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci 100:5772-5777.
    • (2003) Proc Natl Acad Sci , vol.100 , pp. 5772-5777
    • Ma, B.1    Elkayam, T.2    Wolfson, H.3    Nussinov, R.4
  • 12
    • 0034213559 scopus 로고    scopus 로고
    • Conservation of polar residues as hot-spots at protein interfaces
    • Hu Z, Ma B, Wolfson H, Nussinov R (2000) Conservation of polar residues as hot-spots at protein interfaces. Proteins 39:331-342.
    • (2000) Proteins , vol.39 , pp. 331-342
    • Hu, Z.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 13
    • 38549092067 scopus 로고    scopus 로고
    • Hot-Sprint: Database of computational hot spots in protein interfaces
    • Guney E, Tuncbag N, Keskin O, Gursoy A (2008) Hot-Sprint: database of computational hot spots in protein interfaces. Nucleic Acids Res 36(Suppl 1):D662-D666.
    • (2008) Nucleic Acids Res , vol.36 , Issue.SUPPL. 1
    • Guney, E.1    Tuncbag, N.2    Keskin, O.3    Gursoy, A.4
  • 14
    • 66349094681 scopus 로고    scopus 로고
    • Identification of computational hot spots in protein interfaces: Combining solvent accessibility and inter-residue potentials improves the accuracy
    • Tuncbag N, Gursoy A, Keskin O (2009) Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. Bioinformatics 25:1513-1520.
    • (2009) Bioinformatics , vol.25 , pp. 1513-1520
    • Tuncbag, N.1    Gursoy, A.2    Keskin, O.3
  • 15
    • 84861036418 scopus 로고    scopus 로고
    • HotRegion: A database of predicted hot spot clusters
    • Cukuroglu E, Gursoy A, Keskin O (2012) HotRegion: a database of predicted hot spot clusters. Nucleic Acids Res 40:D829-D833.
    • (2012) Nucleic Acids Res , vol.40
    • Cukuroglu, E.1    Gursoy, A.2    Keskin, O.3
  • 16
    • 34548764386 scopus 로고    scopus 로고
    • An automated decision-tree approach to predicting protein interaction hot spots
    • Darnell SJ, Page D, Mitchell C (2007) An automated decision-tree approach to predicting protein interaction hot spots. Proteins: Struct Funct Bioinformatics 68: 813-823.
    • (2007) Proteins: Struct Funct Bioinformatics , vol.68 , pp. 813-823
    • Darnell, S.J.1    Page, D.2    Mitchell, C.3
  • 17
    • 3242879771 scopus 로고    scopus 로고
    • Computational alanine scanning of protein-protein interfaces
    • Kortemme D, Kim T, Baker D (2004) Computational alanine scanning of protein-protein interfaces. Sci STKE 219: pl2.
    • (2004) Sci STKE , vol.219
    • Kortemme, D.1    Kim, T.2    Baker, D.3
  • 18
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
    • Guerois J, Nielsen R, Serrano L (2002) Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 320:369-387.
    • (2002) J Mol Biol , vol.320 , pp. 369-387
    • Guerois, J.1    Nielsen, R.2    Serrano, L.3
  • 19
    • 70749125843 scopus 로고    scopus 로고
    • Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods
    • Lise S, Archambeau C, Pontil M, Jones D (2009) Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods. BMC Bioinformatics 10:365.
    • (2009) BMC Bioinformatics , vol.10 , pp. 365
    • Lise, S.1    Archambeau, C.2    Pontil, M.3    Jones, D.4
  • 20
    • 34547573955 scopus 로고    scopus 로고
    • Protein-protein interaction hotspots carved into sequences
    • Ofran Y, Rost B (2007) Protein-protein interaction hotspots carved into sequences, PLoS Comput Biol 3:e119.
    • (2007) PLoS Comput Biol , vol.3
    • Ofran, Y.1    Rost, B.2
  • 21
    • 0035066602 scopus 로고    scopus 로고
    • A database of alanine mutations and their effects on the free energy of binding in protein interactions
    • Thorn KS, Bogan AA (2001) 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
  • 23
    • 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
  • 24
    • 0031036744 scopus 로고    scopus 로고
    • Human cellular retinoic acid binding proteins: Quantitative analysis of the ligand binding properties of the wild-type and sitedirected mutants
    • Wang L, Li Y, Yan H (1997) Human cellular retinoic acid binding proteins: quantitative analysis of the ligand binding properties of the wild-type and sitedirected mutants. J Biol Chem 272:1541-1547.
    • (1997) J Biol Chem , vol.272 , pp. 1541-1547
    • Wang, L.1    Li, Y.2    Yan, H.3
  • 25
    • 77649228104 scopus 로고    scopus 로고
    • The overlap of small molecule and protein binding sites within families of protein structures
    • Davis FP, Sali A (2010) The overlap of small molecule and protein binding sites within families of protein structures. PLoS Comput Biol 6:e1000668.
    • (2010) PLoS Comput Biol , vol.6
    • Davis, F.P.1    Sali, A.2
  • 26
    • 84865494461 scopus 로고    scopus 로고
    • Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces
    • Zerbe BS, Hall DR, Vajda S, Whitty A, Kozakov D (2012) Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces. J Chem Inform Model 52:2236-2244.
    • (2012) J Chem Inform Model , vol.52 , pp. 2236-2244
    • Zerbe, B.S.1    Hall, D.R.2    Vajda, S.3    Whitty, A.4    Kozakov, D.5
  • 30
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 31
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727-748.
    • (1997) J Mol Biol , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 32
    • 0026813925 scopus 로고
    • The computer program LUDI: A new method for the de novo design of enzyme inhibitors
    • Bohm HJ (1991) The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J Comput-Aided Mol Des 6:61-78.
    • (1991) J Comput-Aided Mol des , vol.6 , pp. 61-78
    • Bohm, H.J.1
  • 34
    • 84863296319 scopus 로고    scopus 로고
    • Algorithmic challenges in structure-based drug design and NMR structural biology
    • Wang L, Zou S, Wang Y (2012) Algorithmic challenges in structure-based drug design and NMR structural biology. Front Electr Electron Eng 7:69-84.
    • (2012) Front Electr Electron Eng , vol.7 , pp. 69-84
    • Wang, L.1    Zou, S.2    Wang, Y.3
  • 35
    • 0031370977 scopus 로고    scopus 로고
    • Ligsite: Automatic and efficient detection of potential small molecule-binding sites in proteins
    • Hendlich M, Rippmann F, Barnickel G (1997) Ligsite: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graph Model 15:359-363.
    • (1997) J Mol Graph Model , vol.15 , pp. 359-363
    • Hendlich, M.1    Rippmann, F.2    Barnickel, G.3
  • 36
    • 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
  • 38
    • 0038642113 scopus 로고    scopus 로고
    • Cripto forms a complex with activin and type ii activin receptors and can block activin signalling
    • Gray PC, Harrison CA, Vale W (2003) Cripto forms a complex with activin and type ii activin receptors and can block activin signalling. Proc Nat Acad Sci 100: 5193-5198.
    • (2003) Proc Nat Acad Sci , vol.100 , pp. 5193-5198
    • Gray, P.C.1    Harrison, C.A.2    Vale, W.3
  • 39
    • 41949137589 scopus 로고    scopus 로고
    • Cripto is a noncompetitive activin antagonist that forms analogous signaling complexes with activin and nodal
    • Kelber JA, Shani G, Booker EC, Vale WW, Gray PC (2008) Cripto is a noncompetitive activin antagonist that forms analogous signaling complexes with activin and nodal. J Biol Chem 283:4490-4500.
    • (2008) J Biol Chem , vol.283 , pp. 4490-4500
    • Kelber, J.A.1    Shani, G.2    Booker, E.C.3    Vale, W.W.4    Gray, P.C.5
  • 40
    • 79959471528 scopus 로고    scopus 로고
    • Alantolactone inhibits cell proliferation by interrupting the interaction between cripto-1 and activin receptor type ii a in activin signaling pathway
    • Shi Y, Bao YL, Wu Y, Yu CL, Huang YX, Sun Y, Zheng LH, Li YX (2011) Alantolactone inhibits cell proliferation by interrupting the interaction between cripto-1 and activin receptor type ii a in activin signaling pathway. J Biomol Screen 16:525-535.
    • (2011) J Biomol Screen , vol.16 , pp. 525-535
    • Shi, Y.1    Bao, Y.L.2    Wu, Y.3    Yu, C.L.4    Huang, Y.X.5    Sun, Y.6    Zheng, L.H.7    Li, Y.X.8
  • 41
    • 0037061646 scopus 로고    scopus 로고
    • Inhibition of protein-protein association by small molecules: Approaches and progress
    • Toogood PL (2001) Inhibition of protein-protein association by small molecules: approaches and progress. J Med Chem 45:1543-1558.
    • (2001) J Med Chem , vol.45 , pp. 1543-1558
    • Toogood, P.L.1


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