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Volumn 9, Issue , 2009, Pages

DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER MODEL; COMPUTER PROGRAM; CONFORMATION; CRYSTAL STRUCTURE; DATA BASE; MOLECULAR LIBRARY; MOLECULAR MECHANICS; SCREENING;

EID: 72749127604     PISSN: None     EISSN: 14726769     Source Type: Journal    
DOI: 10.1186/1472-6769-9-6     Document Type: Article
Times cited : (51)

References (52)
  • 1
    • 11144323163 scopus 로고    scopus 로고
    • Virtual screening of chemical libraries
    • 10.1038/nature03197. 15602552
    • Virtual screening of chemical libraries. BK Shoichet, Nature 2004 432 862 865 10.1038/nature03197 15602552
    • (2004) Nature , vol.432 , pp. 862-865
    • Shoichet, B.K.1
  • 2
    • 35348821202 scopus 로고    scopus 로고
    • Virtual screening strategies in drug discovery
    • 10.1016/j.cbpa.2007.08.033. 17936059
    • Virtual screening strategies in drug discovery. C McInnes, Curr Opin Chem Biol 2007 11 494 502 10.1016/j.cbpa.2007.08.033 17936059
    • (2007) Curr Opin Chem Biol , vol.11 , pp. 494-502
    • McInnes, C.1
  • 3
    • 33749513381 scopus 로고    scopus 로고
    • Receptor-based computational screening of compound databases: The main docking-scoring engines
    • 10.2174/138920306778559377. 17073691
    • Receptor-based computational screening of compound databases: the main docking-scoring engines. O Sperandio MA Miteva F Delfaud BO Villoutreix, Curr Protein Pept Sci 2006 7 369 393 10.2174/138920306778559377 17073691
    • (2006) Curr Protein Pept Sci , vol.7 , pp. 369-393
    • Sperandio, O.1    Miteva, M.A.2    Delfaud, F.3    Villoutreix, B.O.4
  • 4
    • 40049105721 scopus 로고    scopus 로고
    • Essential factors for successful virtual screening
    • 10.2174/138955708783331540. 18220986
    • Essential factors for successful virtual screening. MH Seifert M Lang, Mini Rev Med Chem 2008 8 63 72 10.2174/138955708783331540 18220986
    • (2008) Mini Rev Med Chem , vol.8 , pp. 63-72
    • Seifert, M.H.1    Lang, M.2
  • 5
    • 3242884966 scopus 로고    scopus 로고
    • High-throughput docking as a source of novel drug leads
    • 10.1016/j.cbpa.2004.05.001. 15288245
    • High-throughput docking as a source of novel drug leads. JC Alvarez, Curr Opin Chem Biol 2004 8 365 370 10.1016/j.cbpa.2004.05.001 15288245
    • (2004) Curr Opin Chem Biol , vol.8 , pp. 365-370
    • Alvarez, J.C.1
  • 6
    • 34250332663 scopus 로고    scopus 로고
    • Computer-aided drug design: Integration of structure-based and ligand-based approaches in drug design
    • Computer-aided drug design: Integration of structure-based and ligand-based approaches in drug design. P Prathipati A Dixit AK Saxena, Curr Comp Aided Drug Design 2007 3 341 352
    • (2007) Curr Comp Aided Drug Design , vol.3 , pp. 341-352
    • Prathipati, P.1    Dixit, A.2    Saxena, A.K.3
  • 7
    • 54749090921 scopus 로고    scopus 로고
    • Ligand-based approaches in virtual screening
    • 10.2174/157340908785747456
    • Ligand-based approaches in virtual screening. D Douguet, Curr Comp Aided Drug Design 2008 4 180 190 10.2174/157340908785747456
    • (2008) Curr Comp Aided Drug Design , vol.4 , pp. 180-190
    • Douguet, D.1
  • 8
    • 61949166066 scopus 로고    scopus 로고
    • How similar are similarity searching methods? A principal component analysis of molecular descriptor space
    • 10.1021/ci800249s. 19123924
    • How similar are similarity searching methods? A principal component analysis of molecular descriptor space. A Bender JL Jenkins J Scheiber SC Sukuru M Glick JW Davies, J Chem Inf Model 2009 49 108 119 10.1021/ci800249s 19123924
    • (2009) J Chem Inf Model , vol.49 , pp. 108-119
    • Bender, A.1    Jenkins, J.L.2    Scheiber, J.3    Sukuru, S.C.4    Glick, M.5    Davies, J.W.6
  • 11
    • 53349145331 scopus 로고    scopus 로고
    • FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects
    • 10.1186/1471-2105-9-396. 18816385
    • FAF-Drugs2: free ADME/tox filtering tool to assist drug discovery and chemical biology projects. D Lagorce O Sperandio H Galons MA Miteva BO Villoutreix, BMC Bioinformatics 2008 9 396 10.1186/1471-2105-9-396 18816385
    • (2008) BMC Bioinformatics , vol.9 , pp. 396
    • Lagorce, D.1    Sperandio, O.2    Galons, H.3    Miteva, M.A.4    Villoutreix, B.O.5
  • 12
    • 0023965741 scopus 로고
    • SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
    • SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. D Weininger, J Chem Inf Comput Sci 1988 28 31 36
    • (1988) J Chem Inf Comput Sci , vol.28 , pp. 31-36
    • Weininger, D.1
  • 15
    • 0000490166 scopus 로고
    • From atoms and bonds to three-dimensional atomic coordinates: Automatic model builders
    • 10.1021/cr00023a012
    • From atoms and bonds to three-dimensional atomic coordinates: automatic model builders. J Sadowski J Gasteiger, Chem Rev 1993 93 2567 2581 10.1021/cr00023a012
    • (1993) Chem Rev , vol.93 , pp. 2567-2581
    • Sadowski, J.1    Gasteiger, J.2
  • 16
    • 33745135773 scopus 로고    scopus 로고
    • Recent developments of the chemistry development kit (CDK) - An open-source java library for chemoand bioinformatics
    • 10.2174/138161206777585274. 16796559
    • Recent developments of the chemistry development kit (CDK) - an open-source java library for chemoand bioinformatics. C Steinbeck C Hoppe S Kuhn M Floris R Guha EL Willighagen, Curr Pharm Des 2006 12 2111 2120 10.2174/138161206777585274 16796559
    • (2006) Curr Pharm des , vol.12 , pp. 2111-2120
    • Steinbeck, C.1    Hoppe, C.2    Kuhn, S.3    Floris, M.4    Guha, R.5    Willighagen, E.L.6
  • 17
    • 0347296066 scopus 로고    scopus 로고
    • Assessing the performance of OMEGA with respect to retrieving bioactive conformations
    • 10.1016/S1093-3263(02)00204-8. 12543140
    • Assessing the performance of OMEGA with respect to retrieving bioactive conformations. J Bostrom JR Greenwood J Gottfries, J Mol Graph Model 2003 21 449 462 10.1016/S1093-3263(02)00204-8 12543140
    • (2003) J Mol Graph Model , vol.21 , pp. 449-462
    • Bostrom, J.1    Greenwood, J.R.2    Gottfries, J.3
  • 18
    • 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
    • 10.1021/ci060084g. 16859316
    • Comparative performance assessment of the conformational model generators omega and catalyst: a large-scale survey on the retrieval of protein-bound ligand conformations. J Kirchmair G Wolber C Laggner T Langer, J Chem Inf Model 2006 46 1848 1861 10.1021/ci060084g 16859316
    • (2006) J Chem Inf Model , vol.46 , pp. 1848-1861
    • Kirchmair, J.1    Wolber, G.2    Laggner, C.3    Langer, T.4
  • 19
    • 0035555863 scopus 로고    scopus 로고
    • Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools
    • 10.1023/A:1015930826903. 12160095
    • Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools. J Bostrom, J Comput Aided Mol Des 2001 15 1137 1152 10.1023/A:1015930826903 12160095
    • (2001) J Comput Aided Mol des , vol.15 , pp. 1137-1152
    • Bostrom, J.1
  • 20
    • 39449105474 scopus 로고    scopus 로고
    • Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis
    • 10.1021/ci7002494. 18183967
    • Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis. KA Brameld B Kuhn DC Reuter M Stahl, J Chem Inf Model 2008 48 1 24 10.1021/ci7002494 18183967
    • (2008) J Chem Inf Model , vol.48 , pp. 1-24
    • Brameld, K.A.1    Kuhn, B.2    Reuter, D.C.3    Stahl, M.4
  • 21
    • 72749091491 scopus 로고    scopus 로고
    • Corina Molecular Networks, GmbH Computerchemie Langemarckplatz 1, Erlangen, Germany
    • Corina. Corina Molecular Networks, GmbH Computerchemie Langemarckplatz 1, Erlangen, Germany 2000
    • (2000) Corina
  • 23
    • 18344382014 scopus 로고    scopus 로고
    • Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms
    • 10.1021/ci049753l. 15807508
    • Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms. J Kirchmair C Laggner G Wolber T Langer, J Chem Inf Model 2005 45 422 430 10.1021/ci049753l 15807508
    • (2005) J Chem Inf Model , vol.45 , pp. 422-430
    • Kirchmair, J.1    Laggner, C.2    Wolber, G.3    Langer, T.4
  • 24
    • 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
    • 10.1016/j.ejmech.2008.09.052. 19022539
    • MED-3DMC: a new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space. O Sperandio M Souaille F Delfaud MA Miteva BO Villoutreix, Eur J Med Chem 2009 44 1405 1409 10.1016/j.ejmech.2008.09.052 19022539
    • (2009) Eur J Med Chem , vol.44 , pp. 1405-1409
    • Sperandio, O.1    Souaille, M.2    Delfaud, F.3    Miteva, M.A.4    Villoutreix, B.O.5
  • 26
    • 37249065124 scopus 로고    scopus 로고
    • Generating conformer ensembles using a multiobjective genetic algorithm
    • 10.1021/ci6005646. 17892278
    • Generating conformer ensembles using a multiobjective genetic algorithm. MJ Vainio MS Johnson, J Chem Inf Model 2007 47 2462 2474 10.1021/ci6005646 17892278
    • (2007) J Chem Inf Model , vol.47 , pp. 2462-2474
    • Vainio, M.J.1    Johnson, M.S.2
  • 28
    • 35248863951 scopus 로고    scopus 로고
    • CAESAR: A new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration
    • 10.1021/ci700136x. 17691764
    • CAESAR: a new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration. J Li T Ehlers J Sutter S Varma-O'brien J Kirchmair, J Chem Inf Model 2007 47 1923 1932 10.1021/ci700136x 17691764
    • (2007) J Chem Inf Model , vol.47 , pp. 1923-1932
    • Li, J.1    Ehlers, T.2    Sutter, J.3    Varma-O'Brien, S.4    Kirchmair, J.5
  • 29
    • 0242411477 scopus 로고    scopus 로고
    • Tork: Conformational analysis method for molecules and complexes
    • 10.1002/jcc.10325. 14531053
    • Tork: Conformational analysis method for molecules and complexes. CE Chang MK Gilson, J Comput Chem 2003 24 1987 1998 10.1002/jcc.10325 14531053
    • (2003) J Comput Chem , vol.24 , pp. 1987-1998
    • Chang, C.E.1    Gilson, M.K.2
  • 30
    • 84884672735 scopus 로고    scopus 로고
    • San Diego, California
    • Catalyst. San Diego, California
    • Catalyst
  • 31
    • 72749104167 scopus 로고    scopus 로고
    • Molsoft. http://www.molsoft.com/2dto3d.html
    • Molsoft
  • 32
    • 72749113771 scopus 로고    scopus 로고
    • Smiledg. http://iris12.colby.edu/%7Ewww/jme/smiledg.html
    • Smiledg
  • 33
    • 72749117169 scopus 로고    scopus 로고
    • ACD-Create-molecule. http://bioserv.cbs.cnrs.fr/HTML-BIO/APPLET-ACD/ create-molecule.html
    • ACD-Create-molecule
  • 34
    • 72749122041 scopus 로고    scopus 로고
    • Balloon. http://users.abo.fi/mivainio/balloon/
    • Balloon
  • 35
    • 43049146552 scopus 로고    scopus 로고
    • MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening
    • 10.1186/1471-2105-9-184. 18402678
    • MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening. N Sauton D Lagorce BO Villoutreix MA Miteva, BMC Bioinformatics 2008 9 184 10.1186/1471-2105-9-184 18402678
    • (2008) BMC Bioinformatics , vol.9 , pp. 184
    • Sauton, N.1    Lagorce, D.2    Villoutreix, B.O.3    Miteva, M.A.4
  • 36
    • 72749117657 scopus 로고    scopus 로고
    • MTI downloads. http://www.mti.univ-paris-diderot.fr/fr/downloads.html
    • MTI Downloads
  • 37
    • 72749087087 scopus 로고    scopus 로고
    • Multiconf-DOCK program. http://www.mti.univ-paris-diderot.fr/fr/ downloads.html
    • Multiconf-DOCK Program
  • 38
    • 33846919812 scopus 로고    scopus 로고
    • AMMP program. http://www.cs.gsu.edu/∼cscrwh/ammp/ammp.html
    • AMMP Program
  • 40
    • 4043162793 scopus 로고    scopus 로고
    • VEGA - An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming
    • 10.1023/B:JCAM.0000035186.90683.f2. 15368917
    • VEGA - an open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming. A Pedretti L Villa G Vistoli, J Comput Aided Mol Des 2004 18 167 173 10.1023/B:JCAM.0000035186.90683.f2 15368917
    • (2004) J Comput Aided Mol des , vol.18 , pp. 167-173
    • Pedretti, A.1    Villa, L.2    Vistoli, G.3
  • 43
    • 0001752768 scopus 로고    scopus 로고
    • The Cambridge Structural Database: A quarter of a million crystal structures and rising
    • DOI 10.1107/S0108768102003890
    • The Cambridge Structural Database: A quarter of a million crystal structures and rising. FH Allen, Acta Crystallogr Sect B: Struct Sci 2002 B58 380 388 10.1107/S0108768102003890 (Pubitemid 135702674)
    • (2002) Acta Crystallographica Section B: Structural Science , vol.58 , Issue.3 PART 1 , pp. 380-388
    • Allen, F.H.1
  • 45
    • 72749120268 scopus 로고    scopus 로고
    • Open Babel. http://openbabel.sf.net
    • Open Babel
  • 46
    • 72749100011 scopus 로고    scopus 로고
    • myPresto package. http://medals.jp/myPresto/index.html
    • MyPresto Package
  • 47
    • 0030685159 scopus 로고    scopus 로고
    • Molecular mechanics calculations on Rous sarcoma virus protease with peptide substrates
    • 10.1002/pro.5560061110. 9385639
    • Molecular mechanics calculations on Rous sarcoma virus protease with peptide substrates. IT Weber RW Harrison, Protein Sci 1997 6 2365 2374 10.1002/pro.5560061110 9385639
    • (1997) Protein Sci , vol.6 , pp. 2365-2374
    • Weber, I.T.1    Harrison, R.W.2
  • 48
    • 0042041206 scopus 로고
    • UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations
    • 10.1021/ja00051a040
    • UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. AK Rappé CJ Casewit KS Colwell WA Goddard III WM Skiff, J Am Chem Soc 1992 114 10024 10035 10.1021/ja00051a040
    • (1992) J Am Chem Soc , vol.114 , pp. 10024-10035
    • Rappé, A.K.1    Casewit, C.J.2    Colwell, K.S.3    Goddard III, W.A.4    Skiff, W.M.5
  • 50
    • 0030733080 scopus 로고    scopus 로고
    • Conformational analysis using distance geometry methods
    • 10.1016/S1093-3263(97)00014-4. 9346820
    • Conformational analysis using distance geometry Methods: DC Spellmeyer AK Wong MJ Bower JM Blaney, J Mol Graph Model 1997 15 18 36 10.1016/S1093-3263(97) 00014-4 9346820
    • (1997) J Mol Graph Model , vol.15 , pp. 18-36
    • Spellmeyer, D.C.1    Wong, A.K.2    Bower, M.J.3    Blaney, J.M.4
  • 51
    • 0000125764 scopus 로고
    • A new model for calculating atomic charges in molecules
    • 10.1016/S0040-4039(01)94977-9
    • A new model for calculating atomic charges in molecules. J Gasteiger M Marsili, Tetrahedron Lett 1978 19 3181 3184 10.1016/S0040-4039(01)94977-9
    • (1978) Tetrahedron Lett , vol.19 , pp. 3181-3184
    • Gasteiger, J.1    Marsili, M.2
  • 52
    • 72749107531 scopus 로고    scopus 로고
    • Astex dataset. http://www.ccdc.cam.ac.uk/products/life-sciences/gold/ validation/downloads/download.php4
    • Astex Dataset


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.