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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
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

database coverage
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.

crystallography databases
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.

crystallography access
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)
crystallography access9
Crystallography Access

ConQuest

Query Building

crystallography access10
Crystallography Access

ConQuest

Viewing

Results

crystallography access11
Crystallography Access

WebCSD

Coming

soon

crystallography access12
Crystallography Access

WWW-ICSD

Query

Screen

crystallography access13
Crystallography Access

WWW-ICSD

Results

Use the buttons for further information

or to view a structure

crystallography access14
Crystallography Access

WWW-ICSD

Results

crystallography access15
Crystallography Access

CrystalWeb

Search

Form

crystallography access16
Crystallography Access

CrystalWeb Results

Use the buttons for further information

or to view a structure

crystallography access18
Crystallography Access

Search for Spectra Button

crystallography access20
Crystallography Access

ChemSpider Button

crystallography access21
Crystallography Access

ChemSpider Button

crystallography utilities
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.
csd knowledge bases
CSD Knowledge Bases

ISOSTARnon-bonded interactions

csd knowledge bases26
CSD Knowledge Bases

MogulMolecular Geometries

Results and Analysis for target fragment (angle)

View Structure selected from Histogram

database coverage27
Database coverage
  • Structural Data
  • Physical Chemistry
  • Spectroscopy
  • Synthetic Organic Chemistry
  • Procuring Chemical Compounds
  • Links to primary electronic literature
physical chemistry
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.
physical chemistry29
Physical Chemistry

Detherm - Data / Property Coverage

physical chemistry access
Physical Chemistry - Access

Substance/Mixture

DETHERM

  • Client

Version 2007

physical chemistry access31
Physical Chemistry - Access

DETHERM

  • Client

Version 2007

Property Search

physical chemistry access32
Physical Chemistry - Access

Literature Search

DETHERM

  • Client
physical chemistry access33
Physical Chemistry - Access
  • DETHERM
  • Web

Search Options

physical chemistry access34
Physical Chemistry - Access
  • DETHERM
  • Web

Results

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

slide35

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

physical chemistry36
ACD/LabsPhysical 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
database coverage37
Database coverage
  • Structural Data
  • Physical Chemistry
  • Spectroscopy
  • Synthetic Organic Chemistry
  • Procuring Chemical Compounds
  • Links to primary electronic literature
spectroscopy
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
access specinfo
Access - SpecInfo

SpecSurf - Web interface

access specinfo41
Access - SpecInfo

SpecSurf - Web interface - Editors

access acd labs
Access – ACD/Labs

ChemSketch

pc client

Structure

Editor

Can also be used to search other molecule databases.

access acd labs43
Access – ACD/Labs

ChemSketch

Links to

other

databases

access acd labs44
Access – ACD/Labs

ChemSketch

Allows you to log in to the main databases…

… or calculate some properties…

… or generate a name, SMILES or InChI

access acd labs45
Access – ACD/Labs

ChemSketch

3D Viewer

access acd labs46
Access – ACD/Labs

ChemSketch 2D - 3D

access acd labs47
Access – ACD/Labs

ChemSketch

NMR

Spectrum

Viewer

access acd labs48
Access – ACD/Labs

I-Lab - Web interface

access acd labs49
Access – ACD/Labs

I-Lab - Web interface – Drawing Applet

database coverage50
Database coverage
  • Structural Data
  • Physical Chemistry
  • Spectroscopy
  • Synthetic Organic Chemistry
  • Procuring Chemical Compounds
  • Links to primary electronic literature
synthetic organic chemistry
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.
synthetic organic chemistry52
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.
synthetic organic chemistry53
Synthetic Organic Chemistry

SPRESI

Accessed over the Web via SPRESIweb

synthetic organic chemistry54
Synthetic Organic Chemistry

SPRESI

Synthesis Tree Search (STS)

synthetic organic chemistry55
Synthetic Organic Chemistry

SPRESI

Results

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

accelrys databases
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)

accelrys databases57
Accelrys Databases

Query By Form

accelrys databases58
Accelrys Databases

Query Builder

accelrys databases59
Accelrys Databases

Default Forms - Protecting Groups

chemical database service
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

procuring chemical compounds
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

procuring chemical compounds62
Procuring Chemical Compounds

Available Chemicals

Access via the Web using ChemAxon’s Jchem software

procuring chemical compounds63
Procuring Chemical Compounds

Atom Lists and NOT lists are available

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

procuring chemical compounds64
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)
procuring chemical compounds65
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

procuring chemical compounds66
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

procuring chemical compounds67
Procuring Chemical Compounds

Available Chemicals

procuring chemical compounds68
Procuring Chemical Compounds

Screening Compounds

database coverage69
Database coverage
  • Structural Data
  • Physical Chemistry
  • Spectroscopy
  • Synthetic Organic Chemistry
  • Procuring Chemical Compounds
  • Links to primary electronic literature
supporting utilities
Supporting utilities

Literature Linking

  • Single click access to primary literature.
  • Used with CrystalWeb, ICSD-WWW, and ConQuest
  • Link to electronic sources of the article.
supporting utilities71
Supporting utilities

DOI lookup

e.g.

Requires ID/password

Click logos for more information.

supporting utilities74
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

database coverage75
Database coverage
  • Structural Data
  • Spectroscopy
  • Physical Chemistry
  • Synthetic Organic Chemistry
  • Procuring Chemical Compounds
  • Links to primary electronic literature
help support
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:
further information
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
chemical database service78
Chemical Database Service

Thank you for your attention….

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