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2
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33751149652
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Computer-assisted planning of organic syntheses: The second generation of programs
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Ihlenfeldt, W.-D.; Gasteiger, J. Computer-Assisted Planning of Organic Syntheses: The Second Generation of Programs. Angew. Chem., Int. Ed. Engl. 1995, 34, 2613-2633.
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Ihlenfeldt, W.-D.1
Gasteiger, J.2
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3
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37049231053
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Computer-assisted design of complex organic syntheses
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Selected reference: Computer-Assisted Design of Complex Organic Syntheses. Corey, E. J.; Wipke, W. T. Science 1969, 166, 178-192; also see http://lhasa.harvard.edu.
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Science
, vol.166
, pp. 178-192
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Corey, E.J.1
Wipke, W.T.2
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4
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1542465672
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Generating benign alternative syntheses - The synGen program
-
Chapter 10
-
"Generating Benign Alternative Syntheses - the SynGen Program", Henrickson, J. B. ACS Symposium Series #823, Chapter 10, 127-144, 2002; also see http://syngen2.chem.brandeis.edu.
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ACS Symposium Series #823
, vol.823
, pp. 127-144
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Henrickson, J.B.1
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5
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5344278465
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The WODCA system
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Gasteiger, J., Ed.; Springer-Verlag: Heidelberg
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"The WODCA System" Gasteiger, J.; Ihlenfeldt, W. D. In Software-Development in Chemistry 4; Gasteiger, J., Ed.; Springer-Verlag: Heidelberg, 1990, 57-65; also see http://www2.chemie. uni-erlangen.de/software/ wodca/index5.html
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Software-development in Chemistry
, vol.4
, pp. 57-65
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Gasteiger, J.1
Ihlenfeldt, W.D.2
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6
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84860929142
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SysChem Inc, Coeur d'Alene ID, USA.
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SystematiChem, SysChem Inc, Coeur d'Alene ID, USA.; http:// www.syschem.com/.
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SystematiChem
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7
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0002820943
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SPROUT, HIPPO and CAESA: Tools for de novo structure generation and estimation of synthetic accessibility
-
Gillet, V. J.; Myatt, G.; Zsoldos, Z.; Johnson, A. P. SPROUT, HIPPO and CAESA: Tools for de novo structure generation and estimation of synthetic accessibility. Perspect. Drug Discov. Des. 1995, 3, 34-50; also see http://www.simbiosys.ca/caesa/index.html.
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Perspect. Drug Discov. Des.
, vol.3
, pp. 34-50
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Gillet, V.J.1
Myatt, G.2
Zsoldos, Z.3
Johnson, A.P.4
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8
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0003981102
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Computer-assisted mechanistic evaluation of organic reactions. 1. Overview
-
Selected reference: Salatin, T. D.; Jorgensen, W. J. Computer-assisted mechanistic evaluation of organic reactions. 1. Overview, J. Org. Chem. 1980 45, 2043-2050; also see http://zarbi.chem.yale.edu/ products/cameo/index.shtml.
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, vol.45
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Salatin, T.D.1
Jorgensen, W.J.2
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9
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0000136168
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Simulation of organic reactions: From the degradation of chemicals to combinatorial synthesis
-
Höllering, R.; Gasteiger, J.; Steinhauer, L.; Schulz, K.-P.; Herwig, A. Simulation of Organic Reactions: From the Degradation of Chemicals to Combinatorial Synthesis. J. Chem. Inf. Comput. Sci. 2000, 40, 482-494.
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J. Chem. Inf. Comput. Sci.
, vol.40
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Höllering, R.1
Gasteiger, J.2
Steinhauer, L.3
Schulz, K.-P.4
Herwig, A.5
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10
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0002557694
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EROS - A computer program for generating sequences of reactions
-
EROS - A Computer Program for Generating Sequences of Reactions Gasteiger, J.; Jochum, C. Topics Curr. Chem. 1978, 74, 93-126; also see http://zabib.chemie.uni-erlangen.de/software/eros/index.html.
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Topics Curr. Chem.
, vol.74
, pp. 93-126
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Gasteiger, J.1
Jochum, C.2
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11
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84860928711
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Daylight chemical information systems
-
Chapter 4, Santa Fe, NM, USA
-
Daylight Theory Manual, Chapter 4, Daylight Chemical Information Systems, Santa Fe, NM, USA; http://www.daylight.com/dayhtml/doc/ theory/theory.smarts. html.
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Daylight Theory Manual
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12
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0004117249
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For example SMARTS see
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For example SMARTS see Daylight Chemical Information Systems: http://www.daylight.com/support/faq/smarts_examples.faq.html.
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Daylight Chemical Information Systems
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-
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13
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84860928711
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Daylight chemical information systems
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Chapter 7, Santa Fe, NM, USA
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Daylight Theory Manual, Chapter 7, Daylight Chemical Information Systems, Santa Fe, NM, USA; http://www.daylight.com/dayhtml/doc/ theory/theory.rxn.html.
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Daylight Theory Manual
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-
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15
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18344364625
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note
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Specifically these reactive functionalities and substructures were excluded: alkyl halides; alkyl, acyl sulfonates, sulfates, etc.; trichloroacetimidate and related derivatives; epoxides, aziridines, etc.; pyrilium salts and related; nitrogen or oxygen halides; sulfur halogen; allenes; ketenes; azo, diazo compounds, azides; nitroso compounds; acyl halides and related; anhydrides, bicarbonates and related; oxysuccinimides and derivatives; isocyanates, carbodiimides and related; isonitriles; activated esters and derivatives; ortho esters (acyclic); sulfinyl, sulfonyl halides, etc.; Michael acceptors; peroxides, disulfides and related; aldehydes, thioaldehydes and related; Schiff bases, imine derivatives; thioesters, thio acids and related; thiols, thiolates; hydrazines; hydroxylamines; sulfonic, sulfinic acids; reactive halo-aryl derivatives.
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-
-
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16
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18344384382
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note
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Specifically these undesired fragments were excluded: any element except C, H, N, O, S, B, F, Cl, Br, I.; nonstandard isotopes of these elements; extended aromatic carbon systems; >=4 halides; fluoroorganic compounds; unbranched chains >=5 atoms; long chain (>=9 carbons); adamantyl; crown ethers; dipeptides; ethylene >=4 units; unbranched, unsubstituted carbon cycle (>=7 atoms); >=4 conjugated double (or aromatic) bonds; >=2 conjugated acetylenes; >=3 nitro groups; >=4 acetales, aminales, ureas, guanidines, carbamates etc.; aminales, hemiaminals (acyclic); quaternary ammonium salts; lactones; thiourea, thioamide, thioketones, and related, etc. (acyclic); more then two halo-substituents per aryl group; more then one nitro group per aryl group, one nitro and two halides per aryl.
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17
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0035289779
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Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
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Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug. Deliv. Rev. 2001, 46, 3-26.
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Adv. Drug. Deliv. Rev.
, vol.46
, pp. 3-26
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Lipinski, C.A.1
Lombardo, F.2
Dominy, B.W.3
Feeney, P.J.4
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18
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18344384926
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We applied the following constraints: 250 < Mwt < 50; HBD < 5; HBA < 7; RotBonds < 8
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We applied the following constraints: 250 < Mwt < 50; HBD < 5; HBA < 7; RotBonds < 8.
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19
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84860928709
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Several enrichment case-studies are described in http://www.sertanty.com/ ddd/SampleEnrichment Studies.pdf.
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14 considering assay type, mode of ligand interaction, binding domain, kinase substrate, experimental assay conditions, and data consistency/reliability and used to develop several kinase eScreen QSAR models; http://www.sertanty. com/prod/software/escreens.html. Several enrichment case-studies are described in http://www.sertanty.com/ddd/ SampleEnrichment Studies.pdf.
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20
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0033127029
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Pharmacophore fingerprinting. 1. Application to QSAR and focused library design
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McGregor, M. J.; Muskal, S. M. Pharmacophore Fingerprinting. 1. Application to QSAR and Focused Library Design. J. Chem. Inf. Comput. Sci. 1999, 39, 569-574.
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J. Chem. Inf. Comput. Sci.
, vol.39
, pp. 569-574
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McGregor, M.J.1
Muskal, S.M.2
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21
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0033630852
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Pharmacophore fingerprinting. 2. Application to primary library design
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McGregor, M. J.; Muskal, S. M. Pharmacophore Fingerprinting. 2. Application to Primary Library Design. J. Chem. Inf. Comput. Sci. 2000, 40, 117-125.
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(2000)
J. Chem. Inf. Comput. Sci.
, vol.40
, pp. 117-125
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McGregor, M.J.1
Muskal, S.M.2
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22
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5544306271
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Application of the pharmPrint methodology to two protein kinases
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Deanda, F.; Stewart, E. L. Application of the PharmPrint Methodology to Two Protein Kinases. J. Chem. Inf. Comput. Sci. 2004, 44, 1803-1809.
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(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 1803-1809
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Deanda, F.1
Stewart, E.L.2
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23
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84860923117
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Available Chemicals Directory. MDL Information Systems Inc., San Leandro, CA, USA
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Available Chemicals Directory. MDL Information Systems Inc., San Leandro, CA, USA; http://www.mdli.com/products/experiment/ available_chem_dir/index.jsp.
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24
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85128248756
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note
-
30 of 0.5 to 0.6 with respect to the MDDR (65K), ACD (45K), a subset of the Sertanty kinase-active knowledgebase (23K) and commercially available (850 K) compounds from only a small subset of 5 reactions generating 14 virtual protocols; results unpublished.
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25
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84860930237
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As an overview and general reference see the "Genetic Algorithms Warehouse": http://geneticalgorithms.ai-depot.com/Tutorial/ Overview.html.
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Genetic Algorithms Warehouse
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26
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0032112107
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Prediction of human intestinal absorption of drug compounds from molecular structure
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Wessel, M. D.; Jurs, P. C.; Tolan, J.W.; Muskal, S. M. Prediction of Human Intestinal Absorption of Drug Compounds from Molecular Structure. J. Chem. Inf. Comput. Sci. 1998, 38, 726-735.
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Wessel, M.D.1
Jurs, P.C.2
Tolan, J.W.3
Muskal, S.M.4
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27
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84951765703
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Prediction of acute mammalian toxicity from molecular structure for a diverse set of substituted anilines using regression analysis and computational neural networks
-
van de Waterbeemd, H., Testa, B.; Folkers, G., Eds.; Wiley-VCH: New York
-
Johnson, S. R.; Jurs, P. C. Prediction of Acute Mammalian Toxicity from Molecular Structure for a Diverse Set of Substituted Anilines Using Regression Analysis and Computational Neural Networks. In Computer-Assisted Lead Finding and Optimization; van de Waterbeemd, H., Testa, B.; Folkers, G., Eds.; Wiley-VCH: New York, 1997; pp 29-48.
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, pp. 29-48
-
-
Johnson, S.R.1
Jurs, P.C.2
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29
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18344364796
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note
-
This model was developed using a training-set of 817 kinase-active compounds and approximately twice that number of diverse allegedly kinase-inactive compounds; at 0.5 cutoff in this binary model (trained with 0.0-inactive; 1.0-active) - 94.6% of actives and 94.7% of inactives are predicted correctly; this is a binary classifier, so no IC50 values were used in model development; results not published.
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30
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0004117249
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1024 bit structural fingerprints were calculated in Daycart 4.8
-
1024 bit structural fingerprints were calculated in Daycart 4.8, Daylight Chemical Information Systems; http://www.daylight.com/products/ daycart.html.
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Daylight Chemical Information Systems
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31
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0033813234
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Discovery of a new class of p38 kinase inhibitors
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Dumas, J.; Sibley, R.; Riedl, B.; Monahan, M. K.; Lee, W.; Lowinger, T. B.; Redman, A. M.; Johnson, J. S.; Kingery-Wood, J.; Wilhelm, S. M.; Smith, R. A.; Bobko, M.; Schoenleber, R.; Ranges, G. E.; Housley, T. J.; Bhargava, A.; Scott, W. J.; Shrikhande, A. Discovery of a New Class of p38 Kinase Inhibitors. Bioorg. Med. Chem. Lett. 2000, 10, 2047-2050.
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Bioorg. Med. Chem. Lett.
, vol.10
, pp. 2047-2050
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Dumas, J.1
Sibley, R.2
Riedl, B.3
Monahan, M.K.4
Lee, W.5
Lowinger, T.B.6
Redman, A.M.7
Johnson, J.S.8
Kingery-Wood, J.9
Wilhelm, S.M.10
Smith, R.A.11
Bobko, M.12
Schoenleber, R.13
Ranges, G.E.14
Housley, T.J.15
Bhargava, A.16
Scott, W.J.17
Shrikhande, A.18
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32
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18344395134
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Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site
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Pargellis, C.; Tong, L.; Churchill, L.; Cirillo, P. F.; Gilmore, T.; Graham, A. G.; Grob, P. M.; Hickey, E. R.; Moss, N.; Pav, S.; Regan, J. Inhibition of p38 MAP Kinase by Utilizing a Novel Allosteric Binding Site. Nat. Struct. Biol. 2002, 9, 268-272.
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Nat. Struct. Biol.
, vol.9
, pp. 268-272
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-
Pargellis, C.1
Tong, L.2
Churchill, L.3
Cirillo, P.F.4
Gilmore, T.5
Graham, A.G.6
Grob, P.M.7
Hickey, E.R.8
Moss, N.9
Pav, S.10
Regan, J.11
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33
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0037019275
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Pyrazole urea-based inhibitors of p38 MAP kinase: From lead compound to clinical candidate
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Regan, J.; Breitfelder, S.; Cirillo, P.; Gilmore, T.; Graham, A. G.; Hickey, E.; Klaus, B.; Madwed, J.; Moriak, M.; Moss, N.; Pargellis, C.; Pav, S.; Proto, A.; Swinamer, A.; Tong, L.; Torcellini, C. Pyrazole Urea-Based Inhibitors of p38 MAP Kinase: From Lead Compound to Clinical Candidate. J. Med. Chem. 2002, 45, 2994-3008.
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, pp. 2994-3008
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Regan, J.1
Breitfelder, S.2
Cirillo, P.3
Gilmore, T.4
Graham, A.G.5
Hickey, E.6
Klaus, B.7
Madwed, J.8
Moriak, M.9
Moss, N.10
Pargellis, C.11
Pav, S.12
Proto, A.13
Swinamer, A.14
Tong, L.15
Torcellini, C.16
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34
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18344371993
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Amide derivatives
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WO0055153 Sep-21, AstraZeneca UK Limited
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Brown, D. S. Amide Derivatives, PCT int. Appl. WO0055153, 2000-Sep-21, AstraZeneca UK Limited.
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PCT Int. Appl.
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Brown, D.S.1
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35
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20944451179
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Triazine kinase inhibitors
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W00125220A1, April-12, Kinetix Pharmaceuticals Inc.
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Selected reference: Bemis, J. E.; Buchanan, J. L.; Dipietro, L. V.; Elbaum, D.; Habgood, G. J.; KIM, J. L.; Marshall, T. L.; Geuns-Meyer, S. D.; Novak, P. M.; Nunes, J. J.; Patel, V. F.; Toledo-Sherman, L. M.; Zhu, X.; Armistead, D. M. Triazine Kinase Inhibitors. PCT Int. Appl. W00125220A1, 2001-April-12, Kinetix Pharmaceuticals Inc.
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PCT Int. Appl.
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Bemis, J.E.1
Buchanan, J.L.2
Dipietro, L.V.3
Elbaum, D.4
Habgood, G.J.5
Kim, J.L.6
Marshall, T.L.7
Geuns-Meyer, S.D.8
Novak, P.M.9
Nunes, J.J.10
Patel, V.F.11
Toledo-Sherman, L.M.12
Zhu, X.13
Armistead, D.M.14
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