Introduction to the Chemical Database Service

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Introduction to the Chemical Database Service
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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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Database coverage

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

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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.

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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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Crystallography Access

• ICSD
• WWW-ICSD - Web based system for ICSD
• CrystalWeb - Web access to all crystal data
• CrystMet
• CrystalWeb

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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.
• Babel remains 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.

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CSD Knowledge Bases

• IsoStar

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CSD Knowledge Bases

• Mogul

Results and Analysis for target fragment (angle)
View Structure selected from Histogram
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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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Database coverage

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

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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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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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Synthetic Organic Chemistry

• Specialist reaction and related databases
• SPG (Synopsys Protecting Groups - 42,132
  reactions)
• SPS (Solid Phase Synthesis - over 23,000
  reactions)
• ChirBase (Chiral separations of enantiomers by
  chromatography - over 60,000 entries)
• BioCatalysis (Biomolecules as Catalysts - over
  41,000 reactions)

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Database coverage

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

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Searching Chemical Catalogues

• ACD (Available Chemicals Directory)
• a database of suppliers of chemicals
  worldwide.
• This is updated every 3 months
• currently contains nearly ½ million unique
  compounds from 683 suppliers.

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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

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Database coverage

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

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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

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Database coverage

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

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

• 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.

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SpecInfo - Access

• SpecSurf - Web interface

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Database coverage

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

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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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Physical Chemistry
Detherm - Data / Property Coverage
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Physical Chemistry - Access

• DETHERM
• Client/Server

Version 2
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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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Database coverage

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

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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.

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Supporting utilities
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Database coverage

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

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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_at_dl.ac.uk or Phone [phone]

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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

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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

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Chemical Database Service

• Thank you for your attention.