CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 1 Introduction to...

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Transcript of CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 1 Introduction to...

  • Slide 1
  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 1 Introduction to the Chemical Database Service
  • Slide 2
  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 2 CDS Overview Grant funded by EPSRC Service free of charge to users Based at Daresbury Lab (CCLRC) Present Service started 1993 4 staff Provide access to data, support and training Currently 4100+ users from 100+ sites
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 3 Database coverage Structural Data Synthetic Organic Chemistry Procuring Chemical Compounds Spectroscopy Physical Chemistry Links to primary electronic literature
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 4 Crystallography Databases Cambridge Structural Database (CSD) Crystal structure data for ~355,000 organic and organo-metallic compounds Inorganic Crystal Structure Database (ICSD) Around 83,000 inorganic structures also includes minerals and (recently) metals & alloys entries. CrystMet Crystal structure data for over 81,000 metals, alloys, intermetallics, etc.
  • Slide 5
  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 5 Crystallography Access CSD X-Windows based graphical CSD Interface - ConQuest (click the chevron symbols to view a related Flash Movie clip) All Data Web access CrystalWeb
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 6 Crystallography Access ICSD WWW-ICSDWWW-ICSD - Web based system for ICSD CrystalWebCrystalWeb - Web access to all crystal data CrystMet CrystalWeb
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 7 Crystallography Utilities Crystallographic file format converters lBedlam is a generalised format converter very similar to the widely used converter program, Babel, but handles crystallographic data better. lBabel remains the package of choice to handle formats for a whole range of molecular modelling packages. Display and Analysis packages lRasmol - A 3D molecular structure viewer. lMercury - The 3D molecular structure viewer designed for use with the Cambridge structural database (CSD). lVISTA CSD package for statistical analysis of geometrical feature. lCrad - A crystal radial distribution calculation program.
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 8 CSD Knowledge Bases IsoStar
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 9 CSD Knowledge Bases Mogul Results and Analysis for target fragment (angle) View Structure selected from Histogram
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 10 Structural Data from 3D models In addition structural information data is being added from modelling and simulation studies Development work is in progress based on the use the IUPAC/NIST Unique Chemical Identifier (INChI) with a pilot study based on the NCI and ACD databases. ACD(Available Chemicals Directory) MDL database with almost 500,000 compounds from commercial catalogues NCI (National Cancer Institute) 213,628 compounds + 3D models NCI Database (126,705 compounds) Plated Compounds Database (139,735 compounds) Cancer Screened Database (37,330 compounds) AIDS Screened Database (42,687 compounds )
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 11 Database coverage Structural Data Synthetic Organic Chemistry Procuring Chemical Compounds Spectroscopy Physical Chemistry Links to primary electronic literature
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 12 Synthetic Organic Chemistry The Service gives easy access to a variety of selected chemical databases that cover over 50 years of published literature. Providing established and current awareness in synthetic organic chemistry, and now contains almost 1,400,000 searchable reactions. Increasing at rate of nearly 100,000 per year.
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 13 Synthetic Organic Chemistry Core Reaction Databases REFLIB ( Reference Library Of Synthetic Methodology ) Consisting of CHC, THEILHEIMER, METALYSIS, CHIRAS, CLF and ORAC/CORE. (nearly 210,000 reactions from 1946 - 1991) CIRX (ChemInform RX - 1992 - present, over 987,000 reactions) DJSM (Derwent Journal of Synthetic Methods 1980 - present 83,905 reactions) ORGSYN (Organic Synthesis 1921-present 5,857 reactions)
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 14 Synthetic Organic Chemistry Specialist reaction and related databases SPG (Synopsys Protecting Groups - 42,132 reactions)SPG SPS (Solid Phase Synthesis - over 23,000 reactions)SPS ChirBase (Chiral separations of enantiomers by chromatography - over 60,000 entries)ChirBase BioCatalysis (Biomolecules as Catalysts - over 41,000 reactions)BioCatalysis
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 15 Database coverage Structural Data Synthetic Organic Chemistry Procuring Chemical Compounds Spectroscopy Physical Chemistry Links to primary electronic literature
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 16 Searching Chemical Catalogues ACD ACD (Available Chemicals Directory) a database of suppliers of chemicals worldwide. This is updated every 3 months currently contains nearly million unique compounds from 683 suppliers.
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 17 Screening Compounds Suppliers SCDSCD (Screening Compounds Database) over 4.6 Million compounds SALOR BIONETMAYBRIDGETIMTEC ASINEX CHEMBRIDGE CHEMDIV CHEMSTAR SPECS INTERBIOSCREEN I.F. LABS ENAMINE MICROSOURCE PHARMEKS VITAS-MBIOTECH AURORA OTAVASPSAUAMBINTER ACB BLOCKS WORLDMOLECULETOSLABARKIVE Searchable by:- Structure, Formula, Molecular Weight, LogP, Number of Donors, Acceptors and Rotational Bonds
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 18 Database coverage Structural Data Synthetic Organic Chemistry Procuring Chemical Compounds Spectroscopy Physical Chemistry Links to primary electronic literature
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 19 Database Access using ISIS ISIS ISIS (ISIS is used for both Reaction & Chemicals database searching) Client/server system (ISIS/Base + ISIS/Draw) Reaction Browser ACD Finder Chemscape Web based system ReactionWeb ACD on web The National Cancer Institute databases are also available via ISIS/Base and the web
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 20 Database coverage Structural Data Synthetic Organic Chemistry Procuring Chemical Compounds Spectroscopy Physical Chemistry Links to primary electronic literature
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 21 Spectroscopy SpecInfo From Chemical Concepts, contains spectral data sets with their associated structure connection tables. A variety of features are available within the program to help with spectrum prediction and searching. The Spectroscopy databases are designed to aid the chemist in structure elucidation and spectral interpretation problems. 13 C NMRHeteroatom NMR 1 H NMRInfra-redMass spectra 102,36943,851117,37920,898138,727
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 22 SpecInfo - Access SpecSurf - Web interfaceSpecSurf
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 23 Database coverage Structural Data Synthetic Organic Chemistry Procuring Chemical Compounds Spectroscopy Physical Chemistry Links to primary electronic literature
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 24 Physical Chemistry DETHERM One of the world's largest thermophysical property databases of pure compounds and compound mixtures Contains ~5 Million data sets for around 118,000 systems (about 24,500 pure substances and 94,000 mixtures) covering more than 500 property fields.
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 25 Physical Chemistry Detherm - Data / Property Coverage
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 26 Physical Chemistry - Access DETHERM Client/Server Version 2
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  • CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 27 Physical Chemistry Client Version 2.0 of the DETHERM Client was made available to CDS users late 2004. It has a better look and feel than previous versions and a number of new features including improved integration with AspenPlus. It support data export in IK-CAPE PPDX (Physical Property Data Exchange format).
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