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Introduction to the Chemical Database Service

Introduction to the Chemical Database Service. 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. Database coverage.

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Introduction to the Chemical Database Service

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  1. Introduction to the 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

  3. Database coverage • Structural Data • Synthetic Organic Chemistry • Procuring Chemical Compounds • Spectroscopy • Physical Chemistry • Links to primary electronic literature

  4. Crystallography Databases Cambridge Structural Database (CSD) Crystal structure data for ~355,000 organic and organo-metallic compounds Inorganic Crystal Structure Database (ICSD) Around83,000 inorganic structures – also includes minerals and (recently) metals & alloys entries. CrystMet Crystal structure data for over81,000 metals, alloys, intermetallics, etc.

  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

  6. Crystallography Access • ICSD WWW-ICSD - Web based system for ICSD CrystalWeb-Web access to all crystal data • CrystMet CrystalWeb

  7. Crystallography Utilities Crystallographic file format converters • Bedlam is a generalised format converter very similar to the widely used converter program, Babel, but handles crystallographic data better. • Babelremains the package of choice to handle formats for a whole range of molecular modelling packages. Display and Analysis packages • Rasmol - A 3D molecular structure viewer. • Mercury - The 3D molecular structure viewer designed for use with the Cambridge structural database (CSD). • VISTA – CSD package for statistical analysis of geometrical feature. • Crad-A crystal radial distribution calculation program.

  8. CSD Knowledge Bases IsoStar

  9. CSD Knowledge Bases Mogul Results and Analysis for target fragment (angle) View Structure selected from Histogram

  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)

  11. Database coverage • Structural Data • Synthetic Organic Chemistry • Procuring Chemical Compounds • Spectroscopy • Physical Chemistry • Links to primary electronic literature

  12. Synthetic Organic Chemistry The Servicegives 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.

  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)

  14. Synthetic Organic Chemistry Specialist reaction and related databases • SPG(Synopsys Protecting Groups-42,132 reactions) • SPS(Solid Phase Synthesis - over23,000 reactions) • ChirBase (Chiral separations of enantiomers by chromatography - over 60,000 entries) • BioCatalysis(Biomolecules as Catalysts - over 41,000 reactions)

  15. Database coverage • Structural Data • Synthetic Organic Chemistry • Procuring Chemical Compounds • Spectroscopy • Physical Chemistry • Links to primary electronic literature

  16. Searching Chemical Catalogues ACD (Available Chemicals Directory) a database of suppliers of chemicals worldwide. • This isupdated every 3 months • currently contains nearly ½ million unique compounds from 683 suppliers.

  17. Screening Compounds Suppliers SCD(Screening Compounds Database) over 4.6 Million compounds SALOR BIONET MAYBRIDGE TIMTEC ASINEX CHEMBRIDGE CHEMDIV CHEMSTAR SPECS INTERBIOSCREEN I.F. LABS ENAMINE MICROSOURCE PHARMEKS VITAS-M BIOTECH AURORA OTAVA SPSAU AMBINTER ACB BLOCKS WORLDMOLECULE TOSLAB ARKIVE Searchable by:- Structure, Formula, Molecular Weight, LogP, Number of Donors, Acceptors and Rotational Bonds

  18. Database coverage • Structural Data • Synthetic Organic Chemistry • Procuring Chemical Compounds • Spectroscopy • Physical Chemistry • Links to primary electronic literature

  19. Database Access using 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

  20. Database coverage • Structural Data • Synthetic Organic Chemistry • Procuring Chemical Compounds • Spectroscopy • Physical Chemistry • Links to primary electronic literature

  21. 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. Spectroscopy The Spectroscopy databases are designed to aid the chemist in structure elucidation and spectral interpretation problems.

  22. SpecInfo - Access SpecSurf - Web interface

  23. Database coverage • Structural Data • Synthetic Organic Chemistry • Procuring Chemical Compounds • Spectroscopy • Physical Chemistry • Links to primary electronic literature

  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.

  25. Physical Chemistry Detherm - Data / Property Coverage

  26. Physical Chemistry - Access DETHERM • Client/Server Version 2

  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).

  28. Database coverage • Structural Data • Synthetic Organic Chemistry • Procuring Chemical Compounds • Spectroscopy • Physical Chemistry • Links to primary electronic literature

  29. Supporting utilities LitLink • Single click access to primary literature. • Used with CrystalWeb, ICSD-WWW, ConQuest, ReactionWeb or ISIS • Link to electronic sources of the article.

  30. Supporting utilities

  31. Database coverage • Structural Data • Synthetic Organic Chemistry • Procuring Chemical Compounds • Spectroscopy • Physical Chemistry • Links to primary electronic literature

  32. Help/support • Website: • http://cds.dl.ac.uk • User Training and Online Information: • Manuals, Tutorials, and arranging Courses • Flash movies • CDS Newsletters • Helpdesk available: • E-mail cdsbb@dl.ac.uk or Phone 01925 603162

  33. Registration • Individual usernames required • You can register online • But registrations must to be verified by your local User Representative or Head of Department • Current Reps List

  34. Further Information • This Powerpoint demonstration is available online • It will be will be augmented and kept up to date • You can access it online via the URL http://cds.dl.ac.uk/overview • Feel free to download this and related material and make it available to colleagues

  35. Chemical Database Service Thank you for your attention….

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