메뉴 건너뛰기




Volumn 6, Issue 3, 2011, Pages 339-351

Three-dimensional structure generators of drug-like compounds: DG-AMMOS, an open-source package

Author keywords

3D generation; free tool; in silico drug design; open source; virtual screening

Indexed keywords

ALGORITHM; BIOINFORMATICS; CHEMICAL STRUCTURE; COMPUTER INTERFACE; COMPUTER MODEL; COMPUTER PROGRAM; DISTANCE GEOMETRY AND AUTOMATED MOLECULAR MECHANICS OPTIMIZATION FOR IN SILICO SCREENING; DRUG CONFORMATION; DRUG DEVELOPMENT; GEOMETRY; MOLECULAR MECHANICS; MOLECULE; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REVIEW; THREE DIMENSIONAL IMAGING; VALIDATION PROCESS;

EID: 79952205891     PISSN: 17460441     EISSN: None     Source Type: Journal    
DOI: 10.1517/17460441.2011.554393     Document Type: Review
Times cited : (8)

References (96)
  • 1
    • 48749127628 scopus 로고    scopus 로고
    • What has virtual screening ever done for drug discovery?
    • Clark DE. What has virtual screening ever done for drug discovery? Expert Opin Drug Discov 2008;3(8):841-51
    • (2008) Expert Opin Drug Discov , vol.3 , Issue.8 , pp. 841-851
    • Clark, D.E.1
  • 2
    • 11144323163 scopus 로고    scopus 로고
    • Virtual screening of chemical libraries
    • DOI 10.1038/nature03197
    • Shoichet BK. Virtual screening of chemical libraries. Nature 2004;432(7019):862-5 (Pubitemid 40037142)
    • (2004) Nature , vol.432 , Issue.7019 , pp. 862-865
    • Shoichet, B.K.1
  • 3
    • 35348821202 scopus 로고    scopus 로고
    • Virtual screening strategies in drug discovery
    • DOI 10.1016/j.cbpa.2007.08.033, PII S1367593107001172
    • McInnes C. Virtual screening strategies in drug discovery. Curr Opin Chem Biol 2007;11(5):494-502 (Pubitemid 47589008)
    • (2007) Current Opinion in Chemical Biology , vol.11 , Issue.5 , pp. 494-502
    • McInnes, C.1
  • 5
    • 40049105721 scopus 로고    scopus 로고
    • Essential factors for successful virtual screening
    • DOI 10.2174/138955708783331540
    • Seifert MH, Lang M. Essential factors for successful virtual screening. Mini Rev Med Chem 2008;8(1):63-72 (Pubitemid 351320931)
    • (2008) Mini-Reviews in Medicinal Chemistry , vol.8 , Issue.1 , pp. 63-72
    • Seifert, M.H.J.1    Lang, M.2
  • 6
    • 41049113277 scopus 로고    scopus 로고
    • Hierarchical structure-based virtual screening for drug design
    • Miteva MA. Hierarchical structure-based virtual screening for drug design. Biotechnol Biotechnol Equip 2008;1:634-8
    • (2008) Biotechnol Biotechnol Equip , vol.1 , pp. 634-638
    • Miteva, M.A.1
  • 7
    • 34447524011 scopus 로고    scopus 로고
    • Structure-based virtual ligand screening with LigandFit: Pose prediction and enrichment of compound collections
    • DOI 10.1002/prot.21405
    • Montes M, Miteva MA, Villoutreix BO. Structure-based virtual ligand screening with LigandFit: pose prediction and enrichment of compound collections. Proteins 2007;68(3):712-25 (Pubitemid 47068310)
    • (2007) Proteins: Structure, Function and Genetics , vol.68 , Issue.3 , pp. 712-725
    • Montes, M.1    Miteva, M.A.2    Villoutreix, B.O.3
  • 8
    • 33749513381 scopus 로고    scopus 로고
    • Receptor-based computational screening of compound databases: The main docking-scoring engines
    • DOI 10.2174/138920306778559377
    • Sperandio O, Miteva MA, Delfaud F, et al. Receptor-based computational screening of compound databases: the main docking-scoring engines. Curr Protein Pept Sci 2006;7(5):369-93 (Pubitemid 44524488)
    • (2006) Current Protein and Peptide Science , vol.7 , Issue.5 , pp. 369-393
    • Sperandio, O.1    Miteva, M.A.2    Delfaud, F.3    Villoutreix, B.O.4
  • 10
    • 43049146552 scopus 로고    scopus 로고
    • MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening
    • Sauton N, Lagorce D, Villoutreix BO, et al. MS-DOCK: accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening. BMC Bioinformatics 2008;9:184
    • (2008) BMC Bioinformatics , vol.9 , pp. 184
    • Sauton, N.1    Lagorce, D.2    Villoutreix, B.O.3
  • 11
    • 0037068532 scopus 로고    scopus 로고
    • Do structurally similar molecules have similar biological activity?
    • Martin YC, Kofron JL, Traphagen LM. Do structurally similar molecules have similar biological activity? J Med Chem 2002;45(19):4350-8
    • (2002) J Med Chem , vol.45 , Issue.19 , pp. 4350-4358
    • Martin, Y.C.1    Kofron, J.L.2    Traphagen, L.M.3
  • 12
    • 61949166066 scopus 로고    scopus 로고
    • How similar are similarity searching methods? A principal component analysis of molecular descriptor space
    • Bender A, Jenkins JL, Scheiber J, et al. How similar are similarity searching methods? A principal component analysis of molecular descriptor space. J Chem Inf Model 2009;49(1):108-19
    • (2009) J Chem Inf Model , vol.49 , Issue.1 , pp. 108-119
    • Bender, A.1    Jenkins, J.L.2    Scheiber, J.3
  • 13
    • 0000353230 scopus 로고    scopus 로고
    • The characterization of chemical structures using molecular properties. A survey
    • Livingstone DJ. The characterization of chemical structures using molecular properties. A survey. J Chem Inf Comput Sci 2000;40(2):195-209
    • (2000) J Chem Inf Comput Sci , vol.40 , Issue.2 , pp. 195-209
    • Livingstone, D.J.1
  • 14
    • 0030534377 scopus 로고
    • Similarity searching in databases of chemical structures
    • Lipkowitz KB, Boyd DB, editors. edition. VCH Publishers NY
    • Downs GM, Willett P. Similarity searching in databases of chemical structures. In: Lipkowitz KB, Boyd DB, editors. edition. Reviews in computational chemistry. VCH Publishers NY; 1995. p. 1-66
    • (1995) Reviews in Computational Chemistry , pp. 1-66
    • Downs, G.M.1    Willett, P.2
  • 15
    • 0026642983 scopus 로고
    • 3D database searching in drug design
    • Martin YC. 3D database searching in drug design. J Med Chem 1992;35(12):2145-54
    • (1992) J Med Chem , vol.35 , Issue.12 , pp. 2145-2154
    • Martin, Y.C.1
  • 16
    • 0030534012 scopus 로고
    • Three-dimensional structure database searches
    • Lipkowitz KB, Boyd DB, editors, edition. VCH Publishers NY
    • Good AC, Mason JS. Three-dimensional structure database searches. In: Lipkowitz KB, Boyd DB, editors, edition. Reviews in computational chemistry. VCH Publishers NY; 1995. p. 67-117
    • (1995) Reviews in Computational Chemistry , pp. 67-117
    • Good, A.C.1    Mason, J.S.2
  • 17
    • 21244468757 scopus 로고    scopus 로고
    • Searching techniques for databases of two- And three-dimensional chemical structures
    • DOI 10.1021/jm0582165
    • Willett P. Searching techniques for databases of two- and three-dimensional chemical structures. J Med Chem 2005;48(13):4183-99 (Pubitemid 40884919)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.13 , pp. 4183-4199
    • Willett, P.1
  • 18
    • 37649009919 scopus 로고    scopus 로고
    • Molecule-pharmacophore superpositioning and pattern matching in computational drug design
    • Wolber G, Seidel T, Bendix F, et al. Molecule-pharmacophore superpositioning and pattern matching in computational drug design. Drug Discov Today 2008;13(1-2):23-9
    • (2008) Drug Discov Today , vol.13 , Issue.1-2 , pp. 23-29
    • Wolber, G.1    Seidel, T.2    Bendix, F.3
  • 19
    • 0029444383 scopus 로고
    • A genetic algorithm for flexible molecular overlay and pharmacophore elucidation
    • Jones G, Willett P, Glen RC. A genetic algorithm for flexible molecular overlay and pharmacophore elucidation. J Comput Aided Mol Des 1995;9(6):532-49
    • (1995) J Comput Aided Mol Des , vol.9 , Issue.6 , pp. 532-549
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 20
    • 79952234544 scopus 로고    scopus 로고
    • version 2.2
    • OpenEyes ROCS version 2.2. 2006
    • (2006) OpenEyes ROCS
  • 21
    • 70349745554 scopus 로고    scopus 로고
    • Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity
    • Quintus F, Sperandio O, Grynberg J, et al. Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity. BMC Bioinformatics 2009;10:245
    • (2009) BMC Bioinformatics , vol.10 , pp. 245
    • Quintus, F.1    Sperandio, O.2    Grynberg, J.3
  • 23
    • 78650727351 scopus 로고    scopus 로고
    • Conformations and 3D pharmacophore searching
    • In press
    • Schwab CH. Conformations and 3D pharmacophore searching. Drug Discov Today Technologies 2010; In press
    • (2010) Drug Discov Today Technologies
    • Schwab, C.H.1
  • 24
    • 77952326917 scopus 로고    scopus 로고
    • A collaborative database and computational models for tuberculosis drug discovery
    • Ekins S, Bradford J, Dole K, et al. A collaborative database and computational models for tuberculosis drug discovery. Mol Biosyst 2010;6(5):840-51
    • (2010) Mol Biosyst , vol.6 , Issue.5 , pp. 840-851
    • Ekins, S.1    Bradford, J.2    Dole, K.3
  • 25
    • 33644862638 scopus 로고    scopus 로고
    • Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: Ranking, voting, and consensus scoring
    • DOI 10.1021/jm050468i
    • Zhang Q, Muegge I. Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: ranking, voting, and consensus scoring. J Med Chem 2006;49(5):1536-48 (Pubitemid 43376501)
    • (2006) Journal of Medicinal Chemistry , vol.49 , Issue.5 , pp. 1536-1548
    • Zhang, Q.1    Muegge, I.2
  • 26
    • 78650689245 scopus 로고    scopus 로고
    • Comprehensive comparison of ligand-based virtual screening tools against the DUD data set reveals limitations of current 3D methods
    • Venkatraman V, Perez-Nueno VI, Mavridis L, et al. Comprehensive comparison of ligand-based virtual screening tools against the DUD data set reveals limitations of current 3D methods. J Chem Inf Model 2010
    • (2010) J Chem Inf Model
    • Venkatraman, V.1    Perez-Nueno, V.I.2    Mavridis, L.3
  • 27
    • 0023965741 scopus 로고
    • SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
    • Weininger D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J Chem Inf Comput Sci 1988;28(1):31-6
    • (1988) J Chem Inf Comput Sci , vol.28 , Issue.1 , pp. 31-36
    • Weininger, D.1
  • 28
    • 0001708959 scopus 로고
    • Description of several chemical structure file formats used by computer programs developed at molecular design limited
    • Dalby A, Nourse JG, Hounshell WD, et al. Description of several chemical structure file formats used by computer programs developed at molecular design limited. J Chem Inf Comput Sci 1992;32:244-55
    • (1992) J Chem Inf Comput Sci , vol.32 , pp. 244-255
    • Dalby, A.1    Nourse, J.G.2    Hounshell, W.D.3
  • 29
    • 77957894400 scopus 로고    scopus 로고
    • CoCoCo: A free suite of multiconformational chemical databases for high-throughput virtual screening purposes
    • Del Rio A, Barbosa AJ, Caporuscio F, et al. CoCoCo: a free suite of multiconformational chemical databases for high-throughput virtual screening purposes. Mol Biosyst;6(11):2122-8
    • Mol Biosyst , vol.6 , Issue.11 , pp. 2122-2128
    • Del Rio, A.1    Barbosa, A.J.2    Caporuscio, F.3
  • 30
    • 67649619336 scopus 로고    scopus 로고
    • 970 Million druglike small molecules for virtual screening in the chemical universe database GDB-13
    • Blum LC, Reymond JL. 970 million druglike small molecules for virtual screening in the chemical universe database GDB-13. J Am Chem Soc 2009;131(25):8732-3
    • (2009) J Am Chem Soc , vol.131 , Issue.25 , pp. 8732-8733
    • Blum, L.C.1    Reymond, J.L.2
  • 31
    • 77957920721 scopus 로고    scopus 로고
    • Chemical space as a source for new drugs
    • Reymond JL. Chemical space as a source for new drugs. Med Chem Commun 2010;1:30-8
    • (2010) Med Chem Commun , vol.1 , pp. 30-38
    • Reymond, J.L.1
  • 32
    • 0028773372 scopus 로고
    • The conformation of the steroid nucleus. 1950
    • Barton DH. The conformation of the steroid nucleus. 1950. Experientia 1994;50(4):390-4
    • (1994) Experientia , vol.50 , Issue.4 , pp. 390-394
    • Barton, D.H.1
  • 33
    • 0347296066 scopus 로고    scopus 로고
    • Assessing the performance of OMEGA with respect to retrieving bioactive conformations
    • DOI 10.1016/S1093-3263(02)00204-8, PII S1093326302002048
    • Bostrom J, Greenwood JR, Gottfries J. Assessing the performance of OMEGA with respect to retrieving bioactive conformations. J Mol Graph Model 2003;21(5):449-62 (Pubitemid 36120775)
    • (2003) Journal of Molecular Graphics and Modelling , vol.21 , Issue.5 , pp. 449-462
    • Bostrom, J.1    Greenwood, J.R.2    Gottfries, J.3
  • 34
    • 33746921247 scopus 로고    scopus 로고
    • Comparative performance assessment of the conformational model generators omega and catalyst: A large-scale survey on the retrieval of protein-bound ligand conformations
    • DOI 10.1021/ci060084g
    • Kirchmair J, Wolber G, Laggner C, et al. Comparative performance assessment of the conformational model generators omega and catalyst: a large-scale survey on the retrieval of protein-bound ligand conformations. J Chem Inf Model 2006;46(4):1848-61 (Pubitemid 44185709)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.4 , pp. 1848-1861
    • Kirchmair, J.1    Wolber, G.2    Laggner, C.3    Langer, T.4
  • 35
    • 3042806401 scopus 로고    scopus 로고
    • A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
    • DOI 10.1002/prot.20088
    • Perola E, Walters WP, Charifson PS. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins 2004;56(2):235-49 (Pubitemid 38850158)
    • (2004) Proteins: Structure, Function and Genetics , vol.56 , Issue.2 , pp. 235-249
    • Perola, E.1    Walters, W.P.2    Charifson, P.S.3
  • 36
    • 33750434190 scopus 로고    scopus 로고
    • Impact of conformational flexibility on three-dimensional similarity searching using correlation vectors
    • DOI 10.1021/ci050075s
    • Renner S, Schwab CH, Gasteiger J, et al. Impact of conformational flexibility on three-dimensional similarity searching using correlation vectors. J Chem Inf Model 2006;46(6):2324-32 (Pubitemid 46008107)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.6 , pp. 2324-2332
    • Renner, S.1    Schwab, C.H.2    Gasteiger, J.3    Schneider, G.4
  • 37
    • 0000490166 scopus 로고
    • From atoms and bonds to three-dimensional atomic coordinates: Automatic model builders
    • Sadowski J, Gasteiger J. From atoms and bonds to three-dimensional atomic coordinates: automatic model builders. Chem Rev 1993;93:2567-81
    • (1993) Chem Rev , vol.93 , pp. 2567-2581
    • Sadowski, J.1    Gasteiger, J.2
  • 38
    • 33745135773 scopus 로고    scopus 로고
    • Recent developments of the Chemistry Development Kit (CDK) - An open-source Java library for chemo- and bioinformatics
    • DOI 10.2174/138161206777585274
    • Steinbeck C, Hoppe C, Kuhn S, et al. Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics. Curr Pharm Des 2006;12(17):2111-20 (Pubitemid 43891407)
    • (2006) Current Pharmaceutical Design , vol.12 , Issue.17 , pp. 2111-2120
    • Steinbeck, C.1    Hoppe, C.2    Kuhn, S.3    Floris, M.4    Guha, R.5    Willighagen, E.L.6
  • 39
    • 39449105474 scopus 로고    scopus 로고
    • Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis
    • DOI 10.1021/ci7002494
    • Brameld KA, Kuhn B, Reuter DC, et al. Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis. J Chem Inf Model 2008;48(1):1-24 (Pubitemid 351271046)
    • (2008) Journal of Chemical Information and Modeling , vol.48 , Issue.1 , pp. 1-24
    • Brameld, K.A.1    Kuhn, B.2    Reuter, D.C.3    Stahl, M.4
  • 42
    • 79952239011 scopus 로고    scopus 로고
    • Molecular Networks GmbH, Erlangen, Germany
    • The 3D structure generator CORINA.: Molecular Networks GmbH, Erlangen, Germany. 2010
    • (2010) The 3D Structure Generator CORINA
  • 44
    • 18344382014 scopus 로고    scopus 로고
    • Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms
    • DOI 10.1021/ci0497531
    • Kirchmair J, Laggner C, Wolber G, et al. Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms. J Chem Inf Model 2005;45(2):422-30 (Pubitemid 40635351)
    • (2005) Journal of Chemical Information and Modeling , vol.45 , Issue.2 , pp. 422-430
    • Kirchmair, J.1    Laggner, C.2    Wolber, G.3    Langer, T.4
  • 45
    • 61349109390 scopus 로고    scopus 로고
    • MED-3DMC: A new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space
    • Sperandio O, Souaille M, Delfaud F, et al. MED-3DMC: a new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space. Eur J Med Chem 2009;44(4):1405-9
    • (2009) Eur J Med Chem , vol.44 , Issue.4 , pp. 1405-1409
    • Sperandio, O.1    Souaille, M.2    Delfaud, F.3
  • 46
    • 77951987154 scopus 로고    scopus 로고
    • ConfGen: A conformational search method for efficient generation of bioactive conformers
    • Watts KS, Dalal P, Murphy RB, et al. ConfGen: a conformational search method for efficient generation of bioactive conformers. J Chem Inf Model 2010;50(4):534-46
    • (2010) J Chem Inf Model , vol.50 , Issue.4 , pp. 534-546
    • Watts, K.S.1    Dalal, P.2    Murphy, R.B.3
  • 47
    • 37249065124 scopus 로고    scopus 로고
    • Generating conformer ensembles using a multiobjective genetic algorithm
    • DOI 10.1021/Ci6005646
    • Vainio MJ, Johnson MS. Generating conformer ensembles using a multiobjective genetic algorithm. J Chem Inf Model 2007;47(6):2462-74 (Pubitemid 350275111)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.6 , pp. 2462-2474
    • Vainio, M.J.1    Johnson, M.S.2
  • 48
    • 34547594044 scopus 로고    scopus 로고
    • Frog: A FRee Online druG 3D conformation generator (Web Server issue)
    • Leite TB, Gomes D, Miteva MA, et al. Frog: a FRee Online druG 3D conformation generator (Web Server issue). Nucleic Acids Res 2007;35:W568-72
    • (2007) Nucleic Acids Res , vol.35
    • Leite, T.B.1    Gomes, D.2    Miteva, M.A.3
  • 49
    • 77954274184 scopus 로고    scopus 로고
    • Frog2: Efficient 3D conformation ensemble generator for small compounds
    • Miteva MA, Guyon F, Tuffery P. Frog2: efficient 3D conformation ensemble generator for small compounds. Nucleic Acids Res 2010;38(Suppl):W622-7
    • (2010) Nucleic Acids Res , vol.38 , Issue.SUPPL.
    • Miteva, M.A.1    Guyon, F.2    Tuffery, P.3
  • 50
    • 72749127604 scopus 로고    scopus 로고
    • DG-AMMOS: A new tool to generate 3d conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening
    • Lagorce D, Pencheva T, Villoutreix BO, et al. DG-AMMOS: a new tool to generate 3d conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening. BMC Chem Biol 2009;9:6
    • (2009) BMC Chem Biol , vol.9 , pp. 6
    • Lagorce, D.1    Pencheva, T.2    Villoutreix, B.O.3
  • 51
    • 35248863951 scopus 로고    scopus 로고
    • CAESAR: A new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration
    • DOI 10.1021/ci700136x
    • Li J, Ehlers T, Sutter J, et al. CAESAR: a new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration. J Chem Inf Model 2007;47(5):1923-32 (Pubitemid 47561140)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.5 , pp. 1923-1932
    • Li, J.1    Ehlers, T.2    Sutter, J.3    Varma-O'Brien, S.4    Kirchmair, J.5
  • 56
    • 79952203143 scopus 로고    scopus 로고
    • AMMP Available from
    • AMMP. Available from: http://www.cs. gsu.edu/~cscrwh/ammp/ammp.html
  • 58
    • 0030685159 scopus 로고    scopus 로고
    • Molecular mechanics calculations on Rous sarcoma virus protease with peptide substrates
    • Weber IT, Harrison RW. Molecular mechanics calculations on Rous sarcoma virus protease with peptide substrates. Protein Sci 1997;6(11):2365-74 (Pubitemid 27490747)
    • (1997) Protein Science , vol.6 , Issue.11 , pp. 2365-2374
    • Weber, I.T.1    Harrison, R.W.2
  • 59
    • 0024059337 scopus 로고
    • Use of augmented Lagrangians in the calculation of molecular conformations by distance geometry
    • Crippen GM, Smellie AS, Peng JW. Use of augmented Lagrangians in the calculation of molecular conformations by distance geometry. J Chem Inf Comput Sci 1988;28(3):125-8
    • (1988) J Chem Inf Comput Sci , vol.28 , Issue.3 , pp. 125-128
    • Crippen, G.M.1    Smellie, A.S.2    Peng, J.W.3
  • 61
    • 0042041206 scopus 로고
    • UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations
    • Rappé AK, Casewit CJ, Colwell KS, et al. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J Am Chem Soc 1992;114:10024-35
    • (1992) J Am Chem Soc , vol.114 , pp. 10024-10035
    • Rappé, A.K.1    Casewit, C.J.2    Colwell, K.S.3
  • 62
    • 0033001019 scopus 로고    scopus 로고
    • Molecular mechanics analysis of drug-resistant mutants of HIV protease
    • Weber IT, Harrison RW. Molecular mechanics analysis of drug-resistant mutants of HIV protease. Protein Eng 1999;12(6):469-74 (Pubitemid 29322444)
    • (1999) Protein Engineering , vol.12 , Issue.6 , pp. 469-474
    • Weber, I.T.1    Harrison, R.W.2
  • 63
    • 79952210301 scopus 로고    scopus 로고
    • Available from: [Cited]
    • INSERM UMR-S 973 - MTi - Download Section. 2010. Available from: http://www.mti.univ-paris-diderot.fr/en/ downloads.html. [Cited]
    • (2010) INSERM UMR-S 973 - MTi - Download Section
  • 65
    • 79952230054 scopus 로고    scopus 로고
    • Available from: [Cited]
    • DG-AMMOS on Mobyle Portal. 2010. Available from: http://mobyle.rpbs. univ-paris-diderot.fr/cgi-bin/portal.py? form=DG-AMMOS. [Cited]
    • (2010) DG-AMMOS on Mobyle Portal
  • 66
    • 70449403422 scopus 로고    scopus 로고
    • Mobyle: A new full web bioinformatics framework
    • Neron B, Menager H, Maufrais C, et al. Mobyle: a new full web bioinformatics framework. Bioinformatics 2009;25(22):3005-11
    • (2009) Bioinformatics , vol.25 , Issue.22 , pp. 3005-3011
    • Neron, B.1    Menager, H.2    Maufrais, C.3
  • 69
    • 79952204560 scopus 로고    scopus 로고
    • Available from: [Cited]
    • ChemBridge DIVERSetTM collection. 2009; Available from: http://www. chembridge.com/collected-screeninglibraries. html [Cited]
    • (2009) ChemBridge DIVERSetTM Collection
  • 70
    • 53349145331 scopus 로고    scopus 로고
    • FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects
    • Lagorce D, Sperandio O, Galons H, et al. FAF-Drugs2: free ADME/tox filtering tool to assist drug discovery and chemical biology projects. BMC Bioinformatics 2008;9:396
    • (2008) BMC Bioinformatics , vol.9 , pp. 396
    • Lagorce, D.1    Sperandio, O.2    Galons, H.3
  • 73
    • 77649233664 scopus 로고    scopus 로고
    • Rationalizing the chemical space of protein-protein interaction inhibitors
    • Sperandio O, Reynes CH, Camproux AC, et al. Rationalizing the chemical space of protein-protein interaction inhibitors. Drug Discov Today 2010;15(5-6):220-9
    • (2010) Drug Discov Today , vol.15 , Issue.5-6 , pp. 220-229
    • Sperandio, O.1    Reynes, C.H.2    Camproux, A.C.3
  • 74
    • 37249004920 scopus 로고    scopus 로고
    • Reaching for high-hanging fruit in drug discovery at protein-protein interfaces
    • DOI 10.1038/nature06526, PII NATURE06526
    • Wells JA, McClendon CL. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 2007;450(7172):1001-9 (Pubitemid 350273630)
    • (2007) Nature , vol.450 , Issue.7172 , pp. 1001-1009
    • Wells, J.A.1    McClendon, C.L.2
  • 75
    • 74849107544 scopus 로고    scopus 로고
    • Novel organic proteasome inhibitors identified by virtual and in vitro screening
    • Basse N, Montes M, Marechal X, et al. Novel organic proteasome inhibitors identified by virtual and in vitro screening. J Med Chem 2010;53(1):509-13
    • (2010) J Med Chem , vol.53 , Issue.1 , pp. 509-513
    • Basse, N.1    Montes, M.2    Marechal, X.3
  • 76
    • 73449105806 scopus 로고    scopus 로고
    • Prospective ligand- and target-based 3D QSAR: State of the art 2008
    • Clark RD. Prospective ligand- and target-based 3D QSAR: state of the art 2008. Curr Top Med Chem 2009;9(9):791-810
    • (2009) Curr Top Med Chem , vol.9 , Issue.9 , pp. 791-810
    • Clark, R.D.1
  • 77
    • 0037374498 scopus 로고    scopus 로고
    • The price of innovation: New estimates of drug development costs
    • DOI 10.1016/S0167-6296(02)00126-1
    • DiMasi JA, Hansen RW, Grabowski HG. The price of innovation: new estimates of drug development costs. J Health Econ 2003;22(2):151-85 (Pubitemid 36279392)
    • (2003) Journal of Health Economics , vol.22 , Issue.2 , pp. 151-185
    • DiMasi, J.A.1    Hansen, R.W.2    Grabowski, H.G.3
  • 78
    • 33645675960 scopus 로고    scopus 로고
    • Estimating the cost of new drug development: Is it really 802 million dollars?
    • Millwood
    • Adams CP, Brantner VV. Estimating the cost of new drug development: is it really 802 million dollars? Health Aff (Millwood) 2006;25(2):420-8
    • (2006) Health Aff , vol.25 , Issue.2 , pp. 420-428
    • Adams, C.P.1    Brantner, V.V.2
  • 79
    • 0036176766 scopus 로고    scopus 로고
    • Rational approach to aids drug design through structural biology
    • DOI 10.1146/annurev.med.53.052901.131947
    • Wlodawer A. Rational approach to AIDS drug design through structural biology. Annu Rev Med 2002;53:595-614 (Pubitemid 34177897)
    • (2002) Annual Review of Medicine , vol.53 , pp. 595-614
    • Wlodawer, A.1
  • 80
    • 0027096411 scopus 로고
    • Non-peptide fibrinogen receptor antagonists. 1. Discovery and design of exosite inhibitors
    • Hartman GD, Egbertson MS, Halczenko W, et al. Non-peptide fibrinogen receptor antagonists. 1. Discovery and design of exosite inhibitors. J Med Chem 1992;35(24):4640-2
    • (1992) J Med Chem , vol.35 , Issue.24 , pp. 4640-4642
    • Hartman, G.D.1    Egbertson, M.S.2    Halczenko, W.3
  • 83
    • 33644857872 scopus 로고    scopus 로고
    • Optimizing the use of open-source software applications in drug discovery
    • DOI 10.1016/S1359-6446(05)03692-5, PII S1359644605036925
    • Geldenhuys WJ, Gaasch KE, Watson M, et al. Optimizing the use of open-source software applications in drug discovery. Drug Discov Today 2006;11(3-4):127-32 (Pubitemid 43375963)
    • (2006) Drug Discovery Today , vol.11 , Issue.3-4 , pp. 127-132
    • Geldenhuys, W.J.1    Gaasch, K.E.2    Watson, M.3    Allen, D.D.4    Van, D.S.C.J.5
  • 84
    • 13544251502 scopus 로고    scopus 로고
    • The case for open-source software in drug discovery
    • DOI 10.1016/S1359-6446(04)03363-X, PII S135964460403363X
    • DeLano WL. The case for open-source software in drug discovery. Drug Discov Today 2005;10(3):213-17 (Pubitemid 40222233)
    • (2005) Drug Discovery Today , vol.10 , Issue.3 , pp. 213-217
    • DeLano, W.L.1
  • 85
    • 78650689245 scopus 로고    scopus 로고
    • Comprehensive comparison of ligand-based virtual screening tools against the DUD data set reveals limitations of current 3D methods
    • Venkatraman V, Perez-Nueno VI, Mavridis L, et al. Comprehensive comparison of ligand-based virtual screening tools against the DUD data set reveals limitations of current 3D methods. J Chem Inf Model
    • J Chem Inf Model
    • Venkatraman, V.1    Perez-Nueno, V.I.2    Mavridis, L.3
  • 86
    • 77956855101 scopus 로고    scopus 로고
    • Biasing conformational ensembles towards bioactive-like conformers for ligand-based drug design
    • Musafia B, Senderowitz H. Biasing conformational ensembles towards bioactive-like conformers for ligand-based drug design. Expert Opin Drug Discov 2010;5(10):943-59
    • (2010) Expert Opin Drug Discov , vol.5 , Issue.10 , pp. 943-959
    • Musafia, B.1    Senderowitz, H.2
  • 87
    • 72949085818 scopus 로고    scopus 로고
    • Bioactive conformational biasing: A new method for focusing conformational ensembles on bioactive-like conformers
    • Musafia B, Senderowitz H. Bioactive conformational biasing: a new method for focusing conformational ensembles on bioactive-like conformers. J Chem Inf Model 2009;49(11):2469-80
    • (2009) J Chem Inf Model , vol.49 , Issue.11 , pp. 2469-2480
    • Musafia, B.1    Senderowitz, H.2
  • 88
    • 77955658562 scopus 로고    scopus 로고
    • Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble
    • Yongye AB, Bender A, Martinez-Mayorga K. Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble. J Comput Aided Mol Des 2010;24(8):675-86
    • (2010) J Comput Aided Mol Des , vol.24 , Issue.8 , pp. 675-686
    • Yongye, A.B.1    Bender, A.2    Martinez-Mayorga, K.3
  • 89
    • 65249106631 scopus 로고    scopus 로고
    • Assessing the geometric diversity of cytochrome P450 ligand conformers by hierarchical clustering with a stop criterion
    • Meslamani JE, Andre F, Petitjean M. Assessing the geometric diversity of cytochrome P450 ligand conformers by hierarchical clustering with a stop criterion. J Chem Inf Model 2009;49(2):330-7
    • (2009) J Chem Inf Model , vol.49 , Issue.2 , pp. 330-337
    • Meslamani, J.E.1    Andre, F.2    Petitjean, M.3
  • 90
    • 84920281252 scopus 로고    scopus 로고
    • Available from
    • KNIME. Konstanz Information Miner. Available from: http://www.knime.org/ knime
    • Konstanz Information Miner
  • 93
    • 0037361967 scopus 로고    scopus 로고
    • The chemistry development kit (CDK): An open-source Java library for chemo-and bioinformatics
    • Steinbeck C, Han Y, Kuhn S, et al. The chemistry development kit (CDK): an open-source Java library for chemo-and bioinformatics. J Chem Inf Comput Sci 2003;43(2):493-500
    • (2003) J Chem Inf Comput Sci , vol.43 , Issue.2 , pp. 493-500
    • Steinbeck, C.1    Han, Y.2    Kuhn, S.3
  • 94
    • 79952223460 scopus 로고    scopus 로고
    • Available from
    • ChemAxon. Available from: www.chemaxon.com. 2009
    • (2009)
  • 95
    • 33745359822 scopus 로고    scopus 로고
    • The blue obelisk-interoperability in chemical informatics
    • Guha R, Howard MT, Hutchison GR, et al. The blue obelisk-interoperability in chemical informatics. J Chem Inf Model 2006;46(3):991-8
    • (2006) J Chem Inf Model , vol.46 , Issue.3 , pp. 991-998
    • Guha, R.1    Howard, M.T.2    Hutchison, G.R.3
  • 96
    • 79952237413 scopus 로고    scopus 로고
    • Daylight Chemical Information Systems, Inc.
    • Weininger D. Rubicon 4.9. Daylight Chemical Information Systems, Inc. 2008
    • (2008) Rubicon 4.9
    • Weininger, D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.