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Benchmarking Chemistry Functions within Pharmaceutical Drug Discovery and Preclinical Development
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Virtual Screening an Overview
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The Properties of Known Drugs. 1. Molecular Frameworks
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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, P.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Delivery Rev. 1997, 23, 3-25.
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Can We Learn to Distinguish between "Drug-like" and "Nondrug-like" Molecules?
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Identification of Biological Activity Profiles Using Substructural Analysis and Genetic Algorithms
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Simple Selection Criteria for Drug-like Chemical Matter
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A Scoring Scheme for Discriminating between Drugs and Nondrugs
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Sadowski, J.; Kubinyi, H. A Scoring Scheme for Discriminating between Drugs and Nondrugs. J. Med. Chem. 1998, 41, 3325-3329.
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Drug-like Index: A New Approach To Measure Drug-like Compounds and Their Diversity
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Xu, J.; Stevenson, J. Drug-like Index: A New Approach To Measure Drug-like Compounds and Their Diversity. J. Chem. Inf. Comput. Sci. 2000, 40, 1177-1187.
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Xu, J.1
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Property-Based Design: Optimization of Drug Absorption and Pharmacokinetics
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Van de Waterbeemd, H.; Smith, A. D.; Beamont, K.; Walker, K. D. Property-Based Design: Optimization of Drug Absorption and Pharmacokinetics. J. Med. Chem. 2001, 44, 1313-1333.
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Van de Waterbeemd, H.1
Smith, A.D.2
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15
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0035438391
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Is there a Difference between Leads and Drugs? A Historical Perspective
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Oprea, T. I.; Davis, A. M.; Teague, S. J.; Leeson, P. D. Is there a Difference between Leads and Drugs? A Historical Perspective. J. Chem. Inf. Comput. Sci. 2001, 41, 1308-1315.
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Oprea, T.I.1
Davis, A.M.2
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16
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0141969323
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14600 Catalina Street, San Leandro, CA, 94577
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MACCS-II Drug Data Report (2002.1 version) contains biologically active compounds in the different stages of drug development as presented in the patent literature, journals, meetings and congresses. The database is available from MDL Information Systems Inc., 14600 Catalina Street, San Leandro, CA, 94577. Website: www.mdli.com/products/mddr.html.
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17
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0142003993
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14600 Catalina Street, San Leandro, CA, 94577
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Comprehensive Medicinal Chemistry (2002.1 version) contains compounds used or studied as medicinal agents in humans and pharmaceutical compounds. It is derived from the Drug Compendium in the Pergamon's Comprehensive Medicinal Chemistry. The database is available from MDL Information Systems Inc., 14600 Catalina Street, San Leandro, CA, 94577. Website: http://www.mdli.com/products/cmc.html.
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18
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0141934572
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14600 Catalina Street, San Leandro, CA, 94577
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Available Chemical Directory (2002,1 version) contains grade and bulk chemicals. The database is available from MDL Information Systems Inc., 14600 Catalina Street, San Leandro, CA, 94577. Website: http://www.mdli.com/products/acd.html.
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19
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0141900222
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note
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(19) Oprea (ref 5) concluded that the subset of the reactive compounds in ACD and MDDR have the same property distribution than the remaining set and that their removal from the dataset did not influence the overall property distribution. In this study it was assumed that the pharmacophore distribution is also similar in the each set of compounds.
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20
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0141900218
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note
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Compounds that felt into any of the following classes were removed: MDDR- anesthetic, pulmonary surfactant, contrast medium, sweetener, dental agent, ultraviolet light absorber, radiosensitizer, radioprotector, radiopharmaceutical for brain imaging, imaging agent, pharmaceutical aid, keratolytic, dermatological aid, anti acne, spermicide, vaccine, photosintesizer, antidote, blood substitute, chemoprotective, wound healing agent, MoAb, lubricant agent. CMC- buffer, solvent, anesthetic, disinfectant, aerosol propellant, surfactant, preservative, surgical aid, radiopaque medium, X-ray contrast agent, insecticide, astringent, laxative, sweetener, dental caries prophylactic, ultraviolet screen, flavoring agents, chelating agents, radioprotective agent, sequestering agent, imagining agent, repartitioning agent, alkalizing agent, MRI agent, retinal oxygenizing agent, pharmaceutical aid, diagnostic aid, keratolytic agent, veterinary agent, scabicide, ectoparasiticide, nutrient, radiosensitizer, antiseptic, pigment, depigmentor, dermatological aid, antiacne, acaricide, sacaricide, parasiticide, vaccine, photosensitizer, alcohol denaturant, antidote, prosthetic aid, blood substitute, replenister, emulsifier, emollient, detoxicant, antiperspirant, iodine source, emulsifier.
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21
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5344244908
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Chemical Similarity Searching
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Willet, P. Chemical Similarity Searching. J. Chem. Inf. Comput. Sci. 1998, 38, 983-996.
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Willet, P.1
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0142003994
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UNITY 4.3, Tripos Inc., 1699 South Hanley Rd., St. Louis, MO 63144, U.S.A.
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UNITY 4.3, Tripos Inc., 1699 South Hanley Rd., St. Louis, MO 63144, U.S.A.
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23
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0029783934
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Neighborhood Behaviour: A Useful Concept for Validation of "Molecular Diversity" Descriptors
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Patterson, D. E.; Cramer, R. D.; Ferguson, A. M.; Clark, R. D.; Weinberger, L. E. Neighborhood Behaviour: A Useful Concept for Validation of "Molecular Diversity" Descriptors. J. Med. Chem. 1996, 39, 3049-3059.
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Patterson, D.E.1
Cramer, R.D.2
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Clark, R.D.4
Weinberger, L.E.5
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24
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0141969325
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Website: http://www.asinex.com/.
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25
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0142003996
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Website: http://www.maybridge.com/.
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0141969326
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note
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Compounds with Cox activity were identified using an in house literature database covering the last 10 years of the Journal of Medicinal Chemistry publication. Compounds displaying either COX-1 or COX-2 activity were included in the set.
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27
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0033559918
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Hydrogen Bonding, Hydrophobic Interactions, and Failure of the Rigid Receptor Hypothesis
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Davis, A. M.; Teague, S. J. Hydrogen Bonding, Hydrophobic Interactions, and Failure of the Rigid Receptor Hypothesis, Angew. Chem., Int. Ed. Engl. 1999, 38, 736-749.
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Davis, A.M.1
Teague, S.J.2
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0141934577
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note
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SLN, a notation developed by Tripos Inc., 1699 South Hanley Rd., St. Louis, MO 63144, U.S.A. was inspired by the SMILE annotation and has several extensions and modifications allowing specification of full substructure queries, including Markush structures. SLN provides access to the fragment recognition routines from within a procedural language such as SYBYL Programming Language (SPL).
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29
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0142003995
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note
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The SLN definitions used in this work, a modification of the original set provided by Tripos with Syby16.8, are available in Appendix 1. It was necessary to modify the default file to introduce the negatively ionizable and positively ionizable groups and to optimize the hydrogen bond donor/acceptor and hydrophobic definition.
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0142003989
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Syby16.8.1, Tripos Inc., 1699 South Hanley Rd., St. Louis, MO 63144, U.S.A.
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Syby16.8.1, Tripos Inc., 1699 South Hanley Rd., St. Louis, MO 63144, U.S.A.
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0141969324
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The SLN definitions were imported in Syby16.8 as sln3dmacro.def file
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The SLN definitions were imported in Syby16.8 as sln3dmacro.def file.
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32
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37049068888
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Hydrogen Bonding. Part 9. Solute Proton Donor and Proton Acceptor Scales for Use in Drug Design
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Abraham, H. M.; Duce, P. P.; Prior, V. D. Hydrogen Bonding. Part 9. Solute Proton Donor and Proton Acceptor Scales for Use in Drug Design. J. Chem. Soc., Perkin Trans. 2 1989, 1355-1375.
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Abraham, H.M.1
Duce, P.P.2
Prior, V.D.3
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33
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0141934576
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Five- and six-membered rings containing heteroatoms were classified as hydrophobic moieties providing that the heteroatom was not already part of any other functionality
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Five- and six-membered rings containing heteroatoms were classified as hydrophobic moieties providing that the heteroatom was not already part of any other functionality.
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34
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0141967732
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Principle introduced by Vilfredo Pareto in 1897. In this context the principle can be formulated as follows: a minority of causes usually leads to a majority of results
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Principle introduced by Vilfredo Pareto in 1897. In this context the principle can be formulated as follows: a minority of causes usually leads to a majority of results.
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35
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0007182445
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Nicholas Brealy Publisher: London
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Koch, R. The 80/20 Principle; Nicholas Brealy Publisher: London, 1997.
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The 80/20 Principle
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Koch, R.1
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0035324944
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Molecular Complexity and Its mpact on the Probability of Finding Leads for Drug Discovery
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Hann, M. M.; Leach, R. A.; Harper, G. Molecular Complexity and Its mpact on the Probability of Finding Leads for Drug Discovery. J. Chem. Inf. Comput. Sci. 2001, 41, 856-864.
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Hann, M.M.1
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0040914512
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One hundred years of membrane permeability: Does Overton still rule?
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0034256065
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The in silica world of virtual libraries
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Leach, R. A.; Hann, M. M. The in silica world of virtual libraries. Drug Discovery Today 2000, 5, 326-336.
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Leach, R.A.1
Hann, M.M.2
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Property Distributions: Differences between Drugs, Natural Products, and Molecules from Combinatorial Chemistry
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Feher, M.; Schmidt, M. J. Property Distributions: Differences between Drugs, Natural Products, and Molecules from Combinatorial Chemistry. J. Chem. Inf. Comput. Sci. 2003, 43, 218-227.
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Feher, M.1
Schmidt, M.J.2
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41
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0141969322
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The 8251 compounds in the MDDR-L displayed a total of 16920 biological activities grouped in 525 unique indications
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The 8251 compounds in the MDDR-L displayed a total of 16920 biological activities grouped in 525 unique indications.
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