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Introduction to the Chemical Database Service. Introduction. Present Service started 1993. Originally Grant funded by EPSRC but is now a 3 Year contract with EPSRC. 2 Staff covered by contract.

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Introduction to the Chemical Database Service

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Introduction to the chemical database service l.jpg

Introduction to the Chemical Database Service


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Introduction

  • Present Service started 1993

  • Originally Grant funded by EPSRC but is now a 3 Year contract with EPSRC

  • 2 Staff covered by contract

  • Provide networked access to up-to-date, high quality, comprehensive chemistry databases along with support and training

  • Currently over 5,000 users from over 100 sites

  • Service free of charge to users (UK Academics)

free


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Need to be registered user


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Registration


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Access Data


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Database coverage

  • Structural Data

  • Physical Chemistry

  • Spectroscopy

  • Synthetic Organic Chemistry

  • Procuring Chemical Compounds

  • Links to primary electronic literature

ISIS Databases removed May 2007

Databases removed May 2007

What they contain and how you access them.


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Crystallography Databases

Cambridge Structural Database (CSD)

Crystal structure data for 512,881 organic and organo-metallic compounds.

Inorganic Crystal Structure Database (ICSD)

Over132,526 Inorganic structures – also includes minerals and (recently) metals & alloys entries.

CrystMet

Crystal structure data for over126,000 metals, alloys, intermetallics, etc.

Crystal Data Identification File (CDIF)

Crystal class and unit cell data for 237,671 crystal structures.


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Crystallography Access

ICSD – Web access through own interface

WWW-ICSD

  • CSD - X-Windows based graphical Interface via

  • ConQuest

  • All Crystallogrpahy Data - Web accessvia

  • CrystalWeb

  • (click the chevron symbols to view a related Flash Movie clip)


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Crystallography Access

ConQuest

Query Building


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Crystallography Access

ConQuest

Viewing

Results


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Crystallography Access

WebCSD

Coming

soon


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Crystallography Access

WWW-ICSD

Query

Screen


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Crystallography Access

WWW-ICSD

Results

Use the buttons for further information

or to view a structure


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Crystallography Access

WWW-ICSD

Results


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Crystallography Access

CrystalWeb

Search

Form


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Crystallography Access

CrystalWeb Results

Use the buttons for further information

or to view a structure


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Crystallography Access

JMOL Display


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Crystallography Access

Search for Spectra Button


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Crystallography Access


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Crystallography Access

ChemSpider Button


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Crystallography Access

ChemSpider Button


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Crystallography Utilities

Crystallographic file format converters

  • Bedlamis 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.

    Babel and Bedlem are both used by CrystalWeb to provide a wide range of output formats.

    Display and Analysis packages

  • 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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Crystallography Utilities

Mercury


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Crystallography Utilities

VISTA


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CSD Knowledge Bases

ISOSTARnon-bonded interactions


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CSD Knowledge Bases

MogulMolecular Geometries

Results and Analysis for target fragment (angle)

View Structure selected from Histogram


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Database coverage

  • Structural Data

  • Physical Chemistry

  • Spectroscopy

  • Synthetic Organic Chemistry

  • Procuring Chemical Compounds

  • 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 ~6 Million data sets for around 127,000 systems

    (about 26,500 pure substances and 103,000 mixtures)

  • covering more than 500 property fields.


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Physical Chemistry

Detherm - Data / Property Coverage


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Physical Chemistry - Access

Substance/Mixture

DETHERM

  • Client

Version 2007


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Physical Chemistry - Access

DETHERM

  • Client

Version 2007

Property Search


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Physical Chemistry - Access

Literature Search

DETHERM

  • Client


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Physical Chemistry - Access

  • DETHERM

  • Web

    Search Options


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Physical Chemistry - Access

  • DETHERM

  • Web

    Results

It supports data export in IKC-PPDX (Physical Property Data Exchange format).


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Physical Chemistry

ACD/Labs

  • I-Lab allows you to search the database for:-

    • pKa (about 16,000 structures)

    • LogP (over 18,000 structures)

    • Solubility (over 5,000 compounds)

  • A number of physical property predictions are also available:-

  • LogP

  • Aqueous solubility

  • Enthalpy of vaporization

  • Molar Refractivity

  • Parachor

  • Surface Tension

  • Dielectric Constant calculation

  • Monoisotopic Mass

  • Nominal Mass

  • Average Mass

pKa

LogD

Boiling point/Vapour pressure

Adsorption coefficient/

Bioconcentration factor

Molar Volume

Refractive Index

Density

Dielectric Constant calculation

Polarizability


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ACD/Labs

Physical Chemistry

  • In addition, ACD/Labs I-Lab has compound name generation . . .

    • Generate a Name according to IUPAC rules

    • Generate an Index name according to CAS rules

  • Generate a Structure from a chemical name


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Database coverage

  • Structural Data

  • Physical Chemistry

  • Spectroscopy

  • Synthetic Organic Chemistry

  • Procuring Chemical Compounds

  • Links to primary electronic literature


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SpecInfofrom Chemical Concepts,

Searches can be conducted by inputting then matching a

query spectrum (or fragment),

a (sub-) structure or

bibliographic information such as name, formula or CAS number.

Spectroscopy

The Spectroscopy databases are designed to aid the chemist

in structure elucidation and spectral interpretation problems.

  • ACD/Labs

  • ACD/Labs set of databases allows you to draw a (sub)structure and either

  • Search the available NMR databases

  • Predict a spectrum

  • Or search Bibliographic information plus Name, Formula or Molecular Weight


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ACD/Labs

Spectroscopy

SpecInfo


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Access - SpecInfo

SpecSurf - Web interface


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Access - SpecInfo

SpecSurf - Web interface - Editors


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Access – ACD/Labs

ChemSketch

pc client

Structure

Editor

Can also be used to search other molecule databases.


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Access – ACD/Labs

ChemSketch

Links to

other

databases


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Access – ACD/Labs

ChemSketch

Allows you to log in to the main databases…

… or calculate some properties…

… or generate a name, SMILES or InChI


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Access – ACD/Labs

ChemSketch

3D Viewer


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Access – ACD/Labs

ChemSketch 2D - 3D


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Access – ACD/Labs

ChemSketch

NMR

Spectrum

Viewer


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Access – ACD/Labs

I-Lab - Web interface


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Access – ACD/Labs

I-Lab - Web interface – Drawing Applet


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Database coverage

  • Structural Data

  • Physical Chemistry

  • Spectroscopy

  • Synthetic Organic Chemistry

  • Procuring Chemical Compounds

  • Links to primary electronic literature


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Synthetic Organic Chemistry

SPRESI(Storage and Retrieval of Chemical Structure Information)

  • 7.0 million structures

    • 3.9 million reactions

    • 31.7 million factual data entries

  • extracted from:- 645,000 references; 164,000 Patents

  • Contains:-

    • Own drawing package (ICEDIT)

    • Synthesis planning tool.

    • Links with other web sites of interest such as

  • Chemicals Suppliers.


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Synthetic Organic Chemistry

SPRESI

  • Searches can be conducted for:

  • Molecules (Exact, Substructure, Parent, Tautomer,

  • Isomer, Flex Match, Similarity or All-In-One)

  • Reactions(Exact, Substructure, Similar Reaction, All-In- One

  • or Contains Exact Reaction, Reactants or Products)

  • References (e.g. Author, Year, Journal Name, Coden,

  • ISSN, Patent Number).

  • Quick Search - Enter keywords to search through the basic index of structures, reactions and references.


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Synthetic Organic Chemistry

SPRESI

Accessed over the Web via SPRESIweb


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Synthetic Organic Chemistry

SPRESI

Synthesis Tree Search (STS)


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Synthetic Organic Chemistry

SPRESI

Results

Select a supplier from the dropdown list to go to their web site.


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Accelrys Databases

  • BioCatalysis

    Synthesis using enzymes and micro-organisms, which can offer advantages of excellent chemo-, regio- and entantio-selectivity, coupled with important environmental benefits.

  • Protecting Groups

  • Selected protection, deprotection and transprotectionreactions demonstrating the range of conditions under which the reactions can be performed and the conditions under which the protecting groups are stable or labile.

  • Solid Phase Synthesis

  • Information for combinatorial synthesis including information on the Polymer, Substrate and Resin and attachment and detachment conditions.

Accessed using the Accord Database Explorer (Windows only)


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Accelrys Databases

Query By Form


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Accelrys Databases

Query Builder


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Accelrys Databases

Default Forms - Protecting Groups


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Chemical Database Service

Symyx/Isentris Databases - TRIAL

Synthesis Databases

* ChemInform Reaction Library (CIRX)

* Current Synthetic Methodology (CSM)

* Derwent Journal of Synthetic Methods (DJSM)

* ORGSYN Database

* Reference Library of Synthetic Methodology (RefLib)

* Solid-Phase Organic Reactions (SPORE)

Access via

the web (DiscoveryGate) and (Isentris) client.

Sourcing Databases

* Symyx Available Chemicals Directory (ACD)

* Symyx Screening Compounds Directory (SCD)

Bioactivity

e.g. Comprehensive Medicinal Chemistry (CMC)

MDL Drug Data Report (MDDR)

Registry of Toxic Effects of Chemical Substances (RTECS)

Metabolite


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Procuring Chemical Compounds

  • Available Chemicals

  • Searchable catalogue data from several off-the-shelf suppliers:

  • Sigma-Aldrich (Aldrich; Fluka, Riedel, Sigma and Supelco)

  • Acros/Maybridge

  • FluoroChem

  • Apollo

  • Life Chemicals Building Blocks

  • Key Organics Core Scaffold

  • Maybridge Building Blocks

Screening Compounds

over 3.5 Million searchable compounds


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Procuring Chemical Compounds

Available Chemicals

Access via the Web using ChemAxon’s Jchem software


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Procuring Chemical Compounds

Atom Lists and NOT lists are available

There is a tab for Markush structures but are currently not searchable


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Procuring Chemical Compounds

Chemical Terms Filter

Lipinski's rule of five says that, in general, an orally active drug has no more than one violation of the following criteria:

  • Not more than 5 hydrogen bond donors (nitrogen or oxygen atoms

  • with one or more hydrogen atoms)

  • Not more than 10 hydrogen bond acceptors (nitrogen or oxygen atoms)

  • A molecular weight under 500

  • An octanol-water partition coefficient logP of less than 5

  • (Note that all numbers are multiples of five, which is the origin of the rule's name)


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Procuring Chemical Compounds

Chemical Terms Filter

Veber filter (The original “rule of 2”)

The rule predicts a high probability of good oral bioavailability in the rat if a compound has 10 or fewer rotatable bonds and a polar surface area (PSA) equal to or less than 140 Å i.e.

(rotatableBondCount() <= 10) &&

(PSA() <= 140);

J. Chem. Inf. Comput. Sci., 2004, 44 (2), pp 643–651

Lead-likeness:

mass <= 450)

logD("7.4") between -4 and 4

ringCount <= 4

rotatableBondCount <= 10

donorCount <= 5

acceptorCount <= 8

Bioavailability:

mass <= 500

logP <= 5

donorCount <= 5

acceptorCount <= 10

rotatableBondCount <= 10

PSA <= 200

fusedAromaticRingCount <= 5 >= 6


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Procuring Chemical Compounds

Chemical Terms Filter – Drug Likeness

Ghose Filter

mass between 160 and 480

atomCount between 20 and 70

logP between -0.4 and 5.6

refractivity between 40 and 130

More than 80% of the compounds of the Comprehensive Medicinal Chemistry database Ver. 97.1 were found with the filter developed by Ghose.

Muegge filter

mass between 200 and 600

ringCount <= 7

atomCount"6" >= 5 and atomCount - atomCount"6" - atomCount"1" >= 2

rotatableBondCount <= 15

donorCount <= 5

acceptorCount <= 10

logP >= -2 && logP <= 5

PSA <= 150


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Procuring Chemical Compounds

Available Chemicals


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Procuring Chemical Compounds

Screening Compounds


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Database coverage

  • Structural Data

  • Physical Chemistry

  • Spectroscopy

  • Synthetic Organic Chemistry

  • Procuring Chemical Compounds

  • Links to primary electronic literature


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Supporting utilities

Literature Linking

  • Single click access to primary literature.

  • Used with CrystalWeb, ICSD-WWW, and ConQuest

  • Link to electronic sources of the article.


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Supporting utilities

DOI lookup

e.g.

Requires ID/password

Click logos for more information.


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Supporting utilities


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Supporting utilities


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Supporting utilities

Drop-down menus show list of hits and display options

The Journal of Organic Chemistry, 69 (2004) p4500

The link appears here

clickable


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Database coverage

  • Structural Data

  • Spectroscopy

  • Physical Chemistry

  • Synthetic Organic Chemistry

  • Procuring Chemical Compounds

  • Links to primary electronic literature


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Help/support

  • Website: http://cds.dl.ac.uk

  • About the Service: http://cds.dl.ac.uk/cds/service_info/about.html

  • User Training and Online Information:

    • Manuals, Tutorials (e.g. ConQuest, Detherm and SpecSurf) and arranging Courses

    • Flash movies

    • CDS Newsletters

  • Helpdesk available:

    • E-mail cdsbb@dl.ac.uk or Phone 01925 603162


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Further Information

  • This PowerPoint demonstration is available online

  • It 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….


  • Login