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Volumn 104, Issue , 2015, Pages 57-72

Mutational mapping of the transmembrane binding site of the G-protein coupled receptor TGR5 and binding mode prediction of TGR5 agonists

Author keywords

7 Helix receptor; Cyclic AMP; Molecular docking; Molecular dynamics simulations; Quantitative structure activity relationship; Structure model

Indexed keywords

AGENTS INTERACTING WITH TRANSMITTER, HORMONE OR DRUG RECEPTORS; CHOLANE DERIVATIVE; FORSKOLIN; G PROTEIN COUPLED RECEPTOR; G PROTEIN COUPLED RECEPTOR TGR5; G PROTEIN COUPLED RECEPTOR TGR5 AGONIST; HYDROGEN; HYDROXYL GROUP; SODIUM CHLORIDE; TAURINE DERIVATIVE; TAUROCHENODEOXYCHOLIC ACID; TAUROLITHOCHOLIC ACID; TAUROURSODEOXYCHOLIC ACID; UNCLASSIFIED DRUG; BILE ACID; GPBAR1 PROTEIN, HUMAN;

EID: 84943375737     PISSN: 02235234     EISSN: 17683254     Source Type: Journal    
DOI: 10.1016/j.ejmech.2015.09.024     Document Type: Article
Times cited : (25)

References (120)
  • 3
    • 41149144697 scopus 로고    scopus 로고
    • Novel potent and selective bile acid derivatives as TGR5 agonists: Biological screening, structure-activity relationships, and molecular modeling studies
    • H. Sato, A. Macchiarulo, C. Thomas, A. Gioiello, M. Une, A.F. Hofmann, R. Saladin, K. Schoonjans, R. Pellicciari, J. Auwerx, Novel potent and selective bile acid derivatives as TGR5 agonists: biological screening, structure-activity relationships, and molecular modeling studies, J. Med. Chem. 51 (2008) 1831-1841.
    • (2008) J. Med. Chem. , vol.51 , pp. 1831-1841
    • Sato, H.1    Macchiarulo, A.2    Thomas, C.3    Gioiello, A.4    Une, M.5    Hofmann, A.F.6    Saladin, R.7    Schoonjans, K.8    Pellicciari, R.9    Auwerx, J.10
  • 7
    • 70349255713 scopus 로고    scopus 로고
    • The membrane-bound bile acid receptor TGR5 is localized in the epithelium of human gallbladders
    • V. Keitel, K. Cupisti, C. Ullmer, W.T. Knoefel, R. Kubitz, D. Haussinger, The membrane-bound bile acid receptor TGR5 is localized in the epithelium of human gallbladders, Hepatology 50 (2009) 861-870.
    • (2009) Hepatology , vol.50 , pp. 861-870
    • Keitel, V.1    Cupisti, K.2    Ullmer, C.3    Knoefel, W.T.4    Kubitz, R.5    Haussinger, D.6
  • 8
    • 84868360297 scopus 로고    scopus 로고
    • Perspective: TGR5 (Gpbar-1) in liver physiology and disease
    • V. Keitel, D. Haussinger, Perspective: TGR5 (Gpbar-1) in liver physiology and disease, Clin. Res. Hepatol. Gastroenterol. 36 (2012) 412-419.
    • (2012) Clin. Res. Hepatol. Gastroenterol. , vol.36 , pp. 412-419
    • Keitel, V.1    Haussinger, D.2
  • 9
    • 84939815585 scopus 로고    scopus 로고
    • TGR5: Pathogenetic role and/or therapeutic target in fibrosing cholangitis
    • V. Keitel, M. Reich, D. Haussinger, TGR5: pathogenetic role and/or therapeutic target in fibrosing cholangitis Clin. Rev. Allergy Immunol. 48 (2015) 218-225.
    • (2015) Clin. Rev. Allergy Immunol. , vol.48 , pp. 218-225
    • Keitel, V.1    Reich, M.2    Haussinger, D.3
  • 12
    • 79956088562 scopus 로고    scopus 로고
    • The bile acid membrane receptor TGR5 as an emerging target in metabolism and inflammation
    • T.W.H. Pols, L.G. Noriega, M. Nomura, J. Auwerx, K. Schoonjans, The bile acid membrane receptor TGR5 as an emerging target in metabolism and inflammation, J. Hepatol. 54 (2011) 1263-1272.
    • (2011) J. Hepatol. , vol.54 , pp. 1263-1272
    • Pols, T.W.H.1    Noriega, L.G.2    Nomura, M.3    Auwerx, J.4    Schoonjans, K.5
  • 16
    • 34548508190 scopus 로고    scopus 로고
    • Nongenomic actions of bile acids. Synthesis and preliminary characterization of 23-and 6,23-alkylsubstituted bile acid derivatives as selective modulators for the g-protein coupled receptor TGR5
    • R. Pellicciari, H. Sato, A. Gioiello, G. Costantino, A. Macchiarulo, B.M. Sadeghpour, G. Giorgi, K. Schoonjans, J. Auwerx, Nongenomic actions of bile acids. synthesis and preliminary characterization of 23-and 6,23-alkylsubstituted bile acid derivatives as selective modulators for the g-protein coupled receptor TGR5, J. Med. Chem. 50 (2007) 4265-4268.
    • (2007) J. Med. Chem. , vol.50 , pp. 4265-4268
    • Pellicciari, R.1    Sato, H.2    Gioiello, A.3    Costantino, G.4    Macchiarulo, A.5    Sadeghpour, B.M.6    Giorgi, G.7    Schoonjans, K.8    Auwerx, J.9
  • 22
    • 74849119709 scopus 로고    scopus 로고
    • Structureeactivity relationship study of betulinic acid, a novel and selective TGR5 agonist, and its synthetic derivatives: Potential impact in diabetes
    • C. Genet, A. Strehle, C. Schmidt, G. Boudjelal, A. Lobstein, K. Schoonjans, M. Souchet, J. Auwerx, R. Saladin, A. Wagner, Structureeactivity relationship study of betulinic acid, a novel and selective TGR5 agonist, and its synthetic derivatives: potential impact in diabetes, J. Med. Chem. 53 (2009) 178-190.
    • (2009) J. Med. Chem. , vol.53 , pp. 178-190
    • Genet, C.1    Strehle, A.2    Schmidt, C.3    Boudjelal, G.4    Lobstein, A.5    Schoonjans, K.6    Souchet, M.7    Auwerx, J.8    Saladin, R.9    Wagner, A.10
  • 25
    • 77957055780 scopus 로고
    • Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors
    • C.S. Stuart (Ed.) Academic Press
    • J.A. Ballesteros, H. Weinstein. Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors, in: C.S. Stuart (Ed.), Methods Neurosci., Academic Press, 1995, pp. 366-428.
    • (1995) Methods Neurosci , pp. 366-428
    • Ballesteros, J.A.1    Weinstein, H.2
  • 28
    • 0035896038 scopus 로고    scopus 로고
    • Docking ligands onto binding site representations derived from proteins built by homology modelling
    • A. Schafferhans, G. Klebe, Docking ligands onto binding site representations derived from proteins built by homology modelling, J. Mol. Biol. 307 (2001) 407-427.
    • (2001) J. Mol. Biol. , vol.307 , pp. 407-427
    • Schafferhans, A.1    Klebe, G.2
  • 29
    • 84905732337 scopus 로고    scopus 로고
    • Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: Meeting new challenges
    • I. Kufareva, V. Katritch, Raymond C. Stevens, R. Abagyan, Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges, Structure 22 (2014) 1120-1139.
    • (2014) Structure , vol.22 , pp. 1120-1139
    • Kufareva, I.1    Katritch, V.2    Stevens, R.C.3    Abagyan, R.4
  • 30
    • 80051521545 scopus 로고    scopus 로고
    • Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment
    • I. Kufareva, M. Rueda, V. Katritch, R.C. Stevens, R. Abagyan, G.D. Participants, Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment, Structure 19 (2011) 1108-1126.
    • (2011) Structure , vol.19 , pp. 1108-1126
    • Kufareva, I.1    Rueda, M.2    Katritch, V.3    Stevens, R.C.4    Abagyan, R.5    Participants, G.D.6
  • 31
    • 33751099849 scopus 로고    scopus 로고
    • Molecular interaction of serotonin 5-HT2A receptor residues Phe339(6.51) and Phe340(6.52) with superpotent n-benzyl phenethylamine agonists
    • M.R. Braden, J.C. Parrish, J.C. Naylor, D.E. Nichols, Molecular interaction of serotonin 5-HT2A receptor residues Phe339(6.51) and Phe340(6.52) with superpotent n-benzyl phenethylamine agonists, Mol. Pharmacol. 70 (2006) 1956-1964.
    • (2006) Mol. Pharmacol. , vol.70 , pp. 1956-1964
    • Braden, M.R.1    Parrish, J.C.2    Naylor, J.C.3    Nichols, D.E.4
  • 34
    • 0029117219 scopus 로고
    • Identification of critical determinants of a1-adrenergic receptor subtype selective agonist binding
    • J. Hwa, R.M. Graham, D.M. Perez, Identification of critical determinants of a1-adrenergic receptor subtype selective agonist binding, J. Biol. Chem. 270 (1995) 23189-23195.
    • (1995) J. Biol. Chem. , vol.270 , pp. 23189-23195
    • Hwa, J.1    Graham, R.M.2    Perez, D.M.3
  • 35
    • 0032559887 scopus 로고    scopus 로고
    • Human P2-1 receptor: Molecular modeling and site-directed mutagenesis as tools to identify agonist and antagonist recognition sites
    • S. Moro, D. Guo, E. Camaioni, J.L. Boyer, T.K. Harden, K.A. Jacobson, Human P2-1 receptor: molecular modeling and site-directed mutagenesis as tools to identify agonist and antagonist recognition sites, J. Med. Chem. 41 (1998) 1456-1466.
    • (1998) J. Med. Chem. , vol.41 , pp. 1456-1466
    • Moro, S.1    Guo, D.2    Camaioni, E.3    Boyer, J.L.4    Harden, T.K.5    Jacobson, K.A.6
  • 37
    • 84925500666 scopus 로고    scopus 로고
    • Stereoselective synthesis biological evaluation, and modeling of novel bile acid-derived G-protein coupled bile acid receptor 1 (GP-BAR1, TGR5) agonists
    • D.D. Yu, K.M. Sousa, D.L. Mattern, J. Wagner, X. Fu, N. Vaidehi, B.M. Forman, W. Huang, Stereoselective synthesis, biological evaluation, and modeling of novel bile acid-derived G-protein coupled bile acid receptor 1 (GP-BAR1, TGR5) agonists, Bioorg. Med. Chem. 23 (2015) 1613-1628.
    • (2015) Bioorg. Med. Chem. , vol.23 , pp. 1613-1628
    • Yu, D.D.1    Sousa, K.M.2    Mattern, D.L.3    Wagner, J.4    Fu, X.5    Vaidehi, N.6    Forman, B.M.7    Huang, W.8
  • 39
    • 0347123444 scopus 로고    scopus 로고
    • Ligand-supported homology modeling of G-proteincoupled receptor sites: Models sufficient for successful virtual screening
    • A. Evers, G. Klebe, Ligand-supported homology modeling of G-proteincoupled receptor sites: models sufficient for successful virtual screening, Angew. Chem. Int. Ed. 43 (2004) 248-251.
    • (2004) Angew. Chem. Int. Ed. , vol.43 , pp. 248-251
    • Evers, A.1    Klebe, G.2
  • 40
    • 34447136067 scopus 로고    scopus 로고
    • Structure and ligand-binding site characteristics of the human P2-11 nucleotide receptor deduced from computational modelling and mutational analysis
    • J. Zylberg, D. Ecke, B. Fischer, G. Reiser, Structure and ligand-binding site characteristics of the human P2-11 nucleotide receptor deduced from computational modelling and mutational analysis, Biochem. J. 405 (2007) 277-286.
    • (2007) Biochem. J. , vol.405 , pp. 277-286
    • Zylberg, J.1    Ecke, D.2    Fischer, B.3    Reiser, G.4
  • 41
    • 0029043501 scopus 로고
    • Site-directed mutagenesis identifies residues involved in ligand recognition in the human A2a adenosine receptor
    • J. Kim, J. Wess, A.M. van Rhee, T. Schoneberg, K.A. Jacobson, Site-directed mutagenesis identifies residues involved in ligand recognition in the human A2a adenosine receptor, J. Biol. Chem. 270 (1995) 13987-13997.
    • (1995) J. Biol. Chem. , vol.270 , pp. 13987-13997
    • Kim, J.1    Wess, J.2    Van Rhee, A.M.3    Schoneberg, T.4    Jacobson, K.A.5
  • 44
    • 80055007016 scopus 로고    scopus 로고
    • Dissecting the functions of conserved prolines within transmembrane helices of the D2 dopamine receptor
    • E.B. Van Arnam, H.A. Lester, D.A. Dougherty, Dissecting the functions of conserved prolines within transmembrane helices of the D2 dopamine receptor, ACS Chem. Biol. 6 (2011) 1063-1068.
    • (2011) ACS Chem. Biol. , vol.6 , pp. 1063-1068
    • Van Arnam, E.B.1    Lester, H.A.2    Dougherty, D.A.3
  • 47
  • 49
    • 84892517929 scopus 로고    scopus 로고
    • Molecular dynamics simulations and structure-guided mutagenesis provide insight into the architecture of the catalytic core of the ectoine hydroxylase
    • N. Widderich, M. Pittelkow, A. Hoppner, D. Mulnaes, W. Buckel, H. Gohlke, S.H. Smits, E. Bremer, Molecular dynamics simulations and structure-guided mutagenesis provide insight into the architecture of the catalytic core of the ectoine hydroxylase, J. Mol. Biol. 426 (2014) 586-600.
    • (2014) J. Mol. Biol. , vol.426 , pp. 586-600
    • Widderich, N.1    Pittelkow, M.2    Hoppner, A.3    Mulnaes, D.4    Buckel, W.5    Gohlke, H.6    Smits, S.H.7    Bremer, E.8
  • 50
    • 0037046545 scopus 로고    scopus 로고
    • Docking into knowledge-based potential fields: A comparative evaluation of DrugScore
    • C.A. Sotriffer, H. Gohlke, G. Klebe, Docking into knowledge-based potential fields: a comparative evaluation of DrugScore, J. Med. Chem. 45 (2002) 1967-1970.
    • (2002) J. Med. Chem. , vol.45 , pp. 1967-1970
    • Sotriffer, C.A.1    Gohlke, H.2    Klebe, G.3
  • 51
    • 84870030186 scopus 로고    scopus 로고
    • How good are state-of-the-art docking tools in predicting ligand binding modes in proteineprotein interfaces
    • D.M. Krüger, G. Jessen, H. Gohlke, How good are state-of-the-art docking tools in predicting ligand binding modes in proteineprotein interfaces J. Chem. Inf. Model. 52 (2012) 2807-2811.
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2807-2811
    • Krüger, D.M.1    Jessen, G.2    Gohlke, H.3
  • 52
    • 0037068492 scopus 로고    scopus 로고
    • DrugScore meets CoMFA: Adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein
    • H. Gohlke, G. Klebe, DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein, J. Med. Chem. 45 (2002) 4153-4170.
    • (2002) J. Med. Chem. , vol.45 , pp. 4153-4170
    • Gohlke, H.1    Klebe, G.2
  • 53
    • 0037075132 scopus 로고    scopus 로고
    • CoMFA and CoMSIA 3D QSAR and docking studies on conformationally-restrained cinnamoyl HIV-1 integrase inhibitors: Exploration of a binding mode at the active site
    • J.K. Buolamwini, H. Assefa, CoMFA and CoMSIA 3D QSAR and docking studies on conformationally-restrained cinnamoyl HIV-1 integrase inhibitors: exploration of a binding mode at the active site, J. Med. Chem. 45 (2002) 841-852.
    • (2002) J. Med. Chem. , vol.45 , pp. 841-852
    • Buolamwini, J.K.1    Assefa, H.2
  • 54
    • 0028237444 scopus 로고
    • Three-dimensional quantitative structure-activity relationship of human immunodeficiency virus (I) protease inhibitors. 2. Predictive power using limited exploration of alternate binding modes
    • T.I. Oprea, C.L. Waller, G.R. Marshall, Three-dimensional quantitative structure-activity relationship of human immunodeficiency virus (I) protease inhibitors. 2. Predictive power using limited exploration of alternate binding modes, J. Med. Chem. 37 (1994) 2206-2215.
    • (1994) J. Med. Chem. , vol.37 , pp. 2206-2215
    • Oprea, T.I.1    Waller, C.L.2    Marshall, G.R.3
  • 55
    • 12144279076 scopus 로고    scopus 로고
    • Docking and 3-D QSAR studies on indolyl aryl sulfones. Binding mode exploration at the HIV-1 reverse transcriptase non-nucleoside binding site and design of highly active N-(2-hydroxyethyl)carboxamide and N-(2-hydroxyethyl)carbohydrazide derivatives
    • R. Ragno, M. Artico, G. De Martino, G. La Regina, A. Coluccia, A. Di Pasquali, R. Silvestri, Docking and 3-D QSAR studies on indolyl aryl sulfones. Binding mode exploration at the HIV-1 reverse transcriptase non-nucleoside binding site and design of highly active N-(2-hydroxyethyl)carboxamide and N-(2-hydroxyethyl)carbohydrazide derivatives, J. Med. Chem. 48 (2004) 213-223.
    • (2004) J. Med. Chem. , vol.48 , pp. 213-223
    • Ragno, R.1    Artico, M.2    De Martino, G.3    La Regina, G.4    Coluccia, A.5    Di Pasquali, A.6    Silvestri, R.7
  • 56
  • 57
    • 84862276184 scopus 로고    scopus 로고
    • The experimental uncertainty of heterogeneous public Ki data
    • C. Kramer, T. Kalliokoski, P. Gedeck, A. Vulpetti, The experimental uncertainty of heterogeneous public Ki data, J. Med. Chem. 55 (2012) 5165-5173.
    • (2012) J. Med. Chem. , vol.55 , pp. 5165-5173
    • Kramer, C.1    Kalliokoski, T.2    Gedeck, P.3    Vulpetti, A.4
  • 58
    • 0033786003 scopus 로고    scopus 로고
    • Differential modes of agonist binding to 5-hydroxytryptamine2A serotonin receptors revealed by mutation and molecular modeling of conserved residues in transmembrane region 5
    • D.A. Shapiro, K. Kristiansen, W.K. Kroeze, B.L. Roth, Differential modes of agonist binding to 5-hydroxytryptamine2A serotonin receptors revealed by mutation and molecular modeling of conserved residues in transmembrane region 5, Mol. Pharmacol. 58 (2000) 877-886.
    • (2000) Mol. Pharmacol. , vol.58 , pp. 877-886
    • Shapiro, D.A.1    Kristiansen, K.2    Kroeze, W.K.3    Roth, B.L.4
  • 59
    • 0026630139 scopus 로고
    • Serine mutations in transmembrane v of the dopamine D1 receptor affect ligand interactions and receptor activation
    • N.J. Pollock, A.M. Manelli, C.W. Hutchins, M.E. Steffey, R.G. MacKenzie, D.E. Frail, Serine mutations in transmembrane V of the dopamine D1 receptor affect ligand interactions and receptor activation, J. Biol. Chem. 267 (1992) 17780-17786.
    • (1992) J. Biol. Chem. , vol.267 , pp. 17780-17786
    • Pollock, N.J.1    Manelli, A.M.2    Hutchins, C.W.3    Steffey, M.E.4    MacKenzie, R.G.5    Frail, D.E.6
  • 62
    • 84893696729 scopus 로고    scopus 로고
    • A membrane-proximal, C-terminal a-helix is required for plasma membrane localization and function of the G protein-coupled receptor (GPCR) TGR5
    • L. Spomer, C.G.W. Gertzen, B. Schmitz, D. Haussinger, H. Gohlke, V. Keitel, A membrane-proximal, C-terminal a-helix is required for plasma membrane localization and function of the G protein-coupled receptor (GPCR) TGR5, J. Biol. Chem. 289 (2014) 3689-3702.
    • (2014) J. Biol. Chem. , vol.289 , pp. 3689-3702
    • Spomer, L.1    Gertzen, C.G.W.2    Schmitz, B.3    Haussinger, D.4    Gohlke, H.5    Keitel, V.6
  • 68
    • 84929377388 scopus 로고    scopus 로고
    • Regulation of oligomeric organization of the serotonin 5-HT2C receptor observed by spatial intensity distribution analysis
    • R.J. Ward, J.D. Pediani, A.G. Godin, G. Milligan, Regulation of oligomeric organization of the serotonin 5-HT2C receptor observed by spatial intensity distribution analysis, J. Biol. Chem. 290 (2015) 12844-12857.
    • (2015) J. Biol. Chem. , vol.290 , pp. 12844-12857
    • Ward, R.J.1    Pediani, J.D.2    Godin, A.G.3    Milligan, G.4
  • 70
    • 84878665725 scopus 로고    scopus 로고
    • Role of dimerization efficiency of transmembrane domains in activation of fibroblast growth factor receptor 3
    • P.E. Volynsky, A.A. Polyansky, G.N. Fakhrutdinova, E.V. Bocharov, R.G. Efremov, Role of dimerization efficiency of transmembrane domains in activation of fibroblast growth factor receptor 3, J. Am. Chem. Soc. 135 (2013) 8105-8108.
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 8105-8108
    • Volynsky, P.E.1    Polyansky, A.A.2    Fakhrutdinova, G.N.3    Bocharov, E.V.4    Efremov, R.G.5
  • 71
    • 44349091007 scopus 로고    scopus 로고
    • Using multiple templates to improve quality of homology models in automated homology modeling
    • P. Larsson, B. Wallner, E. Lindahl, A. Elofsson, Using multiple templates to improve quality of homology models in automated homology modeling, Protein Sci. 17 (2008) 990-1002.
    • (2008) Protein Sci. , vol.17 , pp. 990-1002
    • Larsson, P.1    Wallner, B.2    Lindahl, E.3    Elofsson, A.4
  • 72
    • 0034327611 scopus 로고    scopus 로고
    • Hinges, swivels and switches: The role of prolines in signalling via transmembrane alpha-helices
    • M.S. Sansom, H. Weinstein, Hinges, swivels and switches: the role of prolines in signalling via transmembrane alpha-helices, Trends Pharmacol. Sci. 21 (2000) 445-451.
    • (2000) Trends Pharmacol. Sci. , vol.21 , pp. 445-451
    • Sansom, M.S.1    Weinstein, H.2
  • 74
    • 41949132916 scopus 로고    scopus 로고
    • Flexible ligand docking to multiple receptor conformations: A practical alternative
    • M. Totrov, R. Abagyan, Flexible ligand docking to multiple receptor conformations: a practical alternative, Curr. Opin. Struct. Biol. 18 (2008) 178-184.
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 178-184
    • Totrov, M.1    Abagyan, R.2
  • 75
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • H. Gohlke, M. Hendlich, G. Klebe, Knowledge-based scoring function to predict protein-ligand interactions, J. Mol. Biol. 295 (2000) 337-356.
    • (2000) J. Mol. Biol. , vol.295 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 76
    • 1942471391 scopus 로고    scopus 로고
    • 3rd Assessing scoring functions for protein-ligand interactions
    • P. Ferrara, H. Gohlke, D.J. Price, G. Klebe, C.L. Brooks 3rd, Assessing scoring functions for protein-ligand interactions, J. Med. Chem. 47 (2004) 3032-3047.
    • (2004) J. Med. Chem. , vol.47 , pp. 3032-3047
    • Ferrara, P.1    Gohlke, H.2    Price, D.J.3    Klebe, G.4    Brooks, C.L.5
  • 77
    • 79960431412 scopus 로고    scopus 로고
    • Target flexibility in RNA-ligand docking modeled by elastic potential grids
    • D.M. Kruger, J. Bergs, S. Kazemi, H. Gohlke, Target flexibility in RNA-ligand docking modeled by elastic potential grids, ACS Med. Chem. Lett. 2 (2011) 489-493.
    • (2011) ACS Med. Chem. Lett. , vol.2 , pp. 489-493
    • Kruger, D.M.1    Bergs, J.2    Kazemi, S.3    Gohlke, H.4
  • 78
    • 68149149959 scopus 로고    scopus 로고
    • Elastic potential grids: Accurate and efficient representation of intermolecular interactions for fully flexible docking
    • S. Kazemi, D.M. Kruger, F. Sirockin, H. Gohlke, Elastic potential grids: accurate and efficient representation of intermolecular interactions for fully flexible docking, Chem Med Chem 4 (2009) 1264-1268.
    • (2009) Chem Med Chem , vol.4 , pp. 1264-1268
    • Kazemi, S.1    Kruger, D.M.2    Sirockin, F.3    Gohlke, H.4
  • 79
    • 0037046545 scopus 로고    scopus 로고
    • Docking into knowledge-based potential fields: A comparative evaluation of DrugScore
    • C.A. Sotriffer, H. Gohlke, G. Klebe, Docking into knowledge-based potential fields: a comparative evaluation of DrugScore, J. Med. Chem. 45 (2002) 1967-1970.
    • (2002) J. Med. Chem. , vol.45 , pp. 1967-1970
    • Sotriffer, C.A.1    Gohlke, H.2    Klebe, G.3
  • 80
    • 84870030186 scopus 로고    scopus 로고
    • How good are state-of-the-art docking tools in predicting ligand binding modes in protein-protein interfaces
    • D.M. Kruger, G. Jessen, H. Gohlke, How good are state-of-the-art docking tools in predicting ligand binding modes in protein-protein interfaces J. Chem. Inf. Model. 52 (2012) 2807-2811.
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2807-2811
    • Kruger, D.M.1    Jessen, G.2    Gohlke, H.3
  • 83
    • 77956394894 scopus 로고    scopus 로고
    • LPA3, a unique G protein-coupled receptor for lysophosphatidic acid
    • K. Hama, J. Aoki, LPA3, a unique G protein-coupled receptor for lysophosphatidic acid, Prog. Lipid Res. 49 (2010) 335-342.
    • (2010) Prog. Lipid Res. , vol.49 , pp. 335-342
    • Hama, K.1    Aoki, J.2
  • 85
    • 33846345695 scopus 로고    scopus 로고
    • Involvement of membrane-type bile acid receptor M-BAR/TGR5 in bile acid-induced activation of epidermal growth factor receptor and mitogen-activated protein kinases in gastric carcinoma cells
    • H. Yasuda, S. Hirata, K. Inoue, H. Mashima, H. Ohnishi, M. Yoshiba, Involvement of membrane-type bile acid receptor M-BAR/TGR5 in bile acid-induced activation of epidermal growth factor receptor and mitogen-activated protein kinases in gastric carcinoma cells, Biochem. Biophys. Res. Commun. 354 (2007) 154-159.
    • (2007) Biochem. Biophys. Res. Commun. , vol.354 , pp. 154-159
    • Yasuda, H.1    Hirata, S.2    Inoue, K.3    Mashima, H.4    Ohnishi, H.5    Yoshiba, M.6
  • 97
    • 0034623005 scopus 로고    scopus 로고
    • T-coffee: A novel method for fast and accurate multiple sequence alignment
    • C. Notredame, D.G. Higgins, J. Heringa, T-coffee: a novel method for fast and accurate multiple sequence alignment, J. Mol. Biol. 302 (2000) 205-217.
    • (2000) J. Mol. Biol. , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 98
  • 101
    • 77956247914 scopus 로고    scopus 로고
    • Chem draw ultra 10.0
    • N. Mills, ChemDraw ultra 10.0, J. Am. Chem. Soc. 128 (2006) 13649-13650.
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 13649-13650
    • Mills, N.1
  • 102
    • 0029315603 scopus 로고
    • MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry
    • P.R. Gerber, K. Müller, MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry, J. Comput. Aided Mol. Des. 9 (1995) 251-268.
    • (1995) J. Comput. Aided Mol. Des. , vol.9 , pp. 251-268
    • Gerber, P.R.1    Müller, K.2
  • 103
    • 0036137713 scopus 로고    scopus 로고
    • Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
    • F. Osterberg, G.M. Morris, M.F. Sanner, A.J. Olson, D.S. Goodsell, Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock, Proteins 46 (2002) 34-40.
    • (2002) Proteins , vol.46 , pp. 34-40
    • Osterberg, F.1    Morris, G.M.2    Sanner, M.F.3    Olson, A.J.4    Goodsell, D.S.5
  • 104
    • 23944499528 scopus 로고    scopus 로고
    • Improving binding mode predictions by docking into protein-specifically adapted potential fields
    • S. Radestock, M. Bohm, H. Gohlke, Improving binding mode predictions by docking into protein-specifically adapted potential fields, J. Med. Chem. 48 (2005) 5466-5479.
    • (2005) J. Med. Chem. , vol.48 , pp. 5466-5479
    • Radestock, S.1    Bohm, M.2    Gohlke, H.3
  • 105
    • 84876174816 scopus 로고    scopus 로고
    • Comparability of mixed IC50 data e a statistical analysis
    • T. Kalliokoski, C. Kramer, A. Vulpetti, P. Gedeck, Comparability of mixed IC50 data e a statistical analysis, PLoS One 8 (2013) e61007.
    • (2013) PLoS One , vol.8 , pp. e61007
    • Kalliokoski, T.1    Kramer, C.2    Vulpetti, A.3    Gedeck, P.4
  • 107
    • 68949149548 scopus 로고    scopus 로고
    • CHARMM-GUI membrane builder for mixed bilayers and its application to yeast membranes
    • S. Jo, J.B. Lim, J.B. Klauda, W. Im, CHARMM-GUI membrane builder for mixed bilayers and its application to yeast membranes, Biophys. J. 97 (2009) 50-58.
    • (2009) Biophys. J. , vol.97 , pp. 50-58
    • Jo, S.1    Lim, J.B.2    Klauda, J.B.3    Im, W.4
  • 109
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
    • C.I. Bayly, P. Cieplak, W. Cornell, P.A. Kollman, A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model, J. Phys. Chem. 97 (1993) 10269-10280.
    • (1993) J. Phys. Chem. , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.3    Kollman, P.A.4
  • 111
    • 84923183676 scopus 로고    scopus 로고
    • Extension of the free energy workflow FEW towards implicit solvent/implicit membrane MMePBSA calculations
    • N. Homeyer, H. Gohlke, Extension of the free energy workflow FEW towards implicit solvent/implicit membrane MMePBSA calculations, Biochim. Biophys. Acta Gen. Subj. 1850 (2015) 972-982.
    • (2015) Biochim. Biophys. Acta Gen. Subj. , vol.1850 , pp. 972-982
    • Homeyer, N.1    Gohlke, H.2
  • 112
    • 84875365821 scopus 로고    scopus 로고
    • FEW: A workflow tool for free energy calculations of ligand binding
    • N. Homeyer, H. Gohlke, FEW: a workflow tool for free energy calculations of ligand binding, J. Comput. Chem. 34 (2013) 965-973.
    • (2013) J. Comput. Chem. , vol.34 , pp. 965-973
    • Homeyer, N.1    Gohlke, H.2
  • 114
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N$log (N) method for Ewald sums in large systems
    • T. Darden, D. York, L. Pedersen, Particle mesh Ewald: an N$log (N) method for Ewald sums in large systems, J. Chem. Phys. 98 (1993) 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 115
    • 36449007976 scopus 로고
    • The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods
    • D.M. York, T.A. Darden, L.G. Pedersen, The effect of long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods, J. Chem. Phys. 99 (1993) 8345-8348.
    • (1993) J. Chem. Phys. , vol.99 , pp. 8345-8348
    • York, D.M.1    Darden, T.A.2    Pedersen, L.G.3
  • 116
    • 84884192184 scopus 로고    scopus 로고
    • Routine microsecond molecular dynamics simulations with Amber on GPUs. 2. Explicit solvent particle mesh Ewald
    • R. Salomon-Ferrer, A.W. Gotz, D. Poole, S. Le Grand, R.C. Walker, Routine microsecond molecular dynamics simulations with Amber on GPUs. 2. Explicit solvent particle mesh Ewald, J. Chem. Theory. Comput. 9 (2013) 3878-3888.
    • (2013) J. Chem. Theory. Comput. , vol.9 , pp. 3878-3888
    • Salomon-Ferrer, R.1    Gotz, A.W.2    Poole, D.3    Le Grand, S.4    Walker, R.C.5
  • 117
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • J.-P. Ryckaert, G. Ciccotti, H.J. Berendsen, Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, J. Comput. Phys. 23 (1977) 327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.3
  • 118
    • 84880022273 scopus 로고    scopus 로고
    • PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data
    • D.R. Roe, T.E. Cheatham III, PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data, J. Chem. Theory. Comput. 9 (2013) 3084-3095.
    • (2013) J. Chem. Theory. Comput. , vol.9 , pp. 3084-3095
    • Roe, D.R.1    Cheatham, T.E.2
  • 119
    • 0029160083 scopus 로고
    • A versatile vector for gene and oligonucleotide transfer into cells in culture and in vivo: Polyethylenimine
    • O. Boussif, F. Lezoualc'h, M.A. Zanta, M.D. Mergny, D. Scherman, B. Demeneix, J.-P. Behr, A versatile vector for gene and oligonucleotide transfer into cells in culture and in vivo: polyethylenimine, PNAS 92 (1995) 7297-7301.
    • (1995) PNAS , vol.92 , pp. 7297-7301
    • Boussif, O.1    Lezoualc'H, F.2    Zanta, M.A.3    Mergny, M.D.4    Scherman, D.5    Demeneix, B.6    Behr, J.-P.7
  • 120
    • 84943398376 scopus 로고    scopus 로고
    • Schrodinger LLC, New York, NY
    • Maestro, in: Schrodinger, LLC, New York, NY, 2014.
    • (2014) Maestro


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