2. WHAT IS CHEMINFORMATICS?
• “Cheminformatics is the combination of chemical synthesis , biological
screening and data mining approaches used to guide drug discovery
and development.”
• “C I is the use of computer software to assist in the acquisition, analysis
and management of data and information relating to chemical
compounds and their properties.”
• CI applies IT to chemical data and includes topics such as chemical
databases, combinatorial library design, structure-activity relationships
and structure based drug design
5. THREE MAJOR ASPECTS OF CHEMINFORMATICS
Information Acquisition, is a process of generating and collecting
data empirically (experimentation) or from theory (molecular
simulation)
Information Management deals with storage and retrieval of
information
Information use, which includes Data Analysis, correlation and
application to problems in the chemical and biochemical sciences
6. CHEMINFORMATICS AND ITS APPLICATIONS
Cheminformatics is a significant application of
information technology to help chemists for
investigating new problems, organize, analyze, and
understand scientific data in the development of
novel compounds, materials and processes.
Primary modules of cheminformatics are
Computer-Assisted Synthesis Design, Structure
representation and Chemmetrics
Cheminformatics
CASD
Structure
Representation
Chemmetrics
7. COMPUTER-ASSISTED SYNTHESIS DESIGN
• Computer-Assisted Synthesis Design (CASD) is applied mainly where artificial
intelligence technique can be applied. This technique is applied in various
applications
• Pharmaceutical industry
• Food industry
• Textile industry
• Agro industry.
8. CHEMICAL STRUCTURE REPRESENTATION
• The chemical structure representations can be linear,
2D or in 3
• SMILES (Simplified Molecular Input Line Entry
Specification) is one of the linear chemical notation
format which is widely used among chemist for
various clinical and analysis purpose.
Structure representation deals with
• Reaction Representation
• Structure Descriptors
• Molecular Modelling
• Structure Searching
• Computer-Assisted Structure Elucidation (CASE)
9. STRUCTURE REPRESENTATION
• Reaction Representation helps to understand the basic chemical models, quantify chemical
reactivity and extract knowledge from the reaction information
• Structure Descriptor used to identify the physical, chemical and biological properties of
chemical compound and relationship between two structures. The descriptors fall into four
classes such as, i) Topological, ii) Geometrical, iii)Electronic and iv) Hybrid or 3D Descriptors
• Molecular modelling is a method includes a variety of computational schemes which are
aimed at stimulating molecular structures, their properties and In- silico behaviour
• Structure Searching involves in determination of features like bond orders, rings and
aromaticity. It includes searching the whole structure, substructure, structure similarity and
diversity.behaviour
• CASE builds on information obtained from various spectroscopic methods like IR, NMR, MS,
etc
10. CHEMMETRICS
• It used for quantitative analyse of the chemical data by
using mathematical and statistical methods
• . It also deals with property prediction of chemical
information
11. APPLICATIONS OF CHEMINFORMATICS
a) Storing data generated through experiments or from molecular
simulation Retrieval of chemical Structures from chemical database
(Software libraries).
b) Prediction of physical, chemical and biological properties of chemical
compounds.
c) Elucidation of the structure of a compound based on spectroscopic data.
d) Structure, Substructure, Similarity and diversity searching from chemical
database
12. APPLICATIONS OF CHEMINFORMATICS
e) High Throughput Screening (HTS) is the integration of technologies
(laboratory automation, assay technology, micro plate based
instrumentation, etc.) to quickly screen chemical compounds in search of a
desired activity.
f) Docking - Interaction between two macromolecules.
g) Drug Discovery.
h) Molecular Science, Materials Science, Food Science (nutraceuticals),
Atmospheric chemistry, Polymer chemistry, Textile Industry, Combinatorial
organic synthesis (COS)
13. ROLE OF CHEMINFORMATICS IN DRUG DISCOVERY
The traditional drug discovery process starts with a particular Disease,
Identification of target, Identification of molecule effective against target and
Preclinical testing. Identification of target and synthesis the molecule to increase
their suitability takes more amounts of time and cost (in millions) which is done in
“WET Lab”.
Cheminformatics play a vital role discovery process of the drug. The
development process starts with human clinical trials, approval from authority and
delivers the product in the market. This process takes about 10-15 years to
discover, develop and bring drug to the market
14. ROLE OF CHEMINFORMATICS IN DRUG DISCOVERY
The modern pharmaceutical drug discovery and development process starts with
Disease selection, Target identification, Lead identification, Lead Optimization, Pre
-clinical trial testing, Clinical trial testing, Approval and circulation (Drug in
market).
In traditional drug discovery phase, the process which cost more time and money
is replaced with lead identification and lead optimization process in modern drug
discovery system. Each phase has an interaction component that transfers data,
knowledge and information to one another
17. CADD
Target protein identification and protein optimization.
• SWISS-MODEL (http://swissmodel.expasy.org/)
• b) Geno3d (http://geno3d-pbil.ibcp.fr)
• c)LOMETS ( http://zhanglab.ccmb.med.umich.edu/LOMETS/)
• d)I-TASSER ( http://zhanglab.ccmb.med.umich.edu/ITASSER/)
18. CADD
• Active sites Prediction
1. Q-Site Finder:Ligand Binding Site Prediction.
(http://bmbpcu36.leeds.ac.uk/qsitefinder/help.html)
2. Sanjeevini (http://www.scfbio-iitd.res.in/sanjeevini/sanjeevini.jsp)
• Ligand preparation and Ligand optimization.
a) Marvin Sketch (http://www.chemaxon.com/products/.)
b) Chem Sketch (http://www.acdlabs.com/products/draw_nom/draw/chemsketch/)
c)Chem writer.(http://metamolecular.com/chemwriter/)
d)CORINA.(http://www.molecular-networks.com/products/corina)
19. CADD
• molecular properties based on the Lipnski's rule and toxicity of the ligand
a)Molinspiration( http://www.molinspiration.com/)
b) OSIRIS Property Explorer
( http://www.organic-chemistry.org/prog/peo/)
c)ALOGPS (http://www.vcclab.org/lab/alogps/)
d)Open-Tox (http://apps.ideaconsult.net:8080/ToxPredict)
20. CADD
• Docking studies
a)Auto dock
b)Dock
c)Gold
d)Swiss Dock
e)Auto dock vina.
f)Schrodinger
g)Hex
h) Argus Lab
• Visualization of docked Complex
a)Pymol.
b)Rasmol.
c)Swiss PDB viewer.
d) Discovery studio
21. TOOLS USED FOR CHEMINFORMATICS
• ISIS-Draw is a chemical structure drawing program for Windows, published by MDL
Information Systems. It is the interfacial software to ISIS/Base database
• ChemDoodle. Chemical structure environment with a main focus on 2D graphics and
publishing to create media for structures, reactions and spectra.
• ChemDraw is a molecule editor developed by the cheminformatics company CambridgeSoft.
ChemDraw is, along with Chem3D and ChemFinder, part of the
• ChemOffice suite of programs and is available for Macintosh and Microsoft Windows .
• ChemWindow, is a chemical structure drawing program with several template. The template
can be created by the customer can be saved in template folder and opened in preference
dialogue box
• ChemSketch, is a chemical structure drawing program with predefined templates are
available for drawing and it is more powerful and user friendly tool for structure analysis.
22. • ChemReader is a software developer toolkit for translating digital raster
images of chemical structures into standard, chemical file formats that
can be searched and analyzed with other open source or commercial
cheminformatic software
• JME Molecular Editor is a Java applet which allows to draw / edit
molecules and reactions (including generation of substructure queries)
and to depict molecules directly within an HTML page
• LogCHEM, an Inductive Logic Programming (ILP) based tool for
discriminative interactive mining of chemical fragments
• PLSR (PLS-Regression), a simple chemmetrics tool, which relates two
matrix X and Y through linear multivariate model and has the ability to
analyse data with many, noisy, collinear, and even incomplete variables in
both X and Y
23. • ChemMine tool is an online service for small molecule analysis. It
provides an interface between cheminformatics and data mining tools for
various analytical analyses in chemical genomics and drug discovery.
• CML (Chemical Markup Language) is degined as combination of semantic
text and nontextual information of chemical strucutre on the internet. It
acts like HTML pages.
• MyChemise (My Chemical Structure Editor) is a new 2D structure editor. It
is designed as a Java applet that enables the direct creation of structures
in the Internet using a web browser. MyChemise saves files in a digital
format (.cse) and the import and export of .mol files using the
appropriate connection tables is also possible.
24. • Open Babel is a chemical tool box which interconverts chemical structures
between different formats, over 110 formats.
• AmberTools is used Biomolecular simulation and analysis of polymers,
nucleotides, and synthetic organic structures.
• Wendi (Web Engine for Nonobvious Drug Information), a web based
integrative data mining tool. It attempts to find non-obvious relationships
between a query compound and scholarly publications, biological
properties, genes and diseases using multiple inform ation sources
• https://www.vls3d.com
25. MOLECULES DATASETS
• PubChem
The world's largest collection of freely available chemical information.
It contains close to 100M compounds and more than 236M
substances. The dataset seems to be well-maintained including
documentation and tutorials. Definitely worth checking out! The link
is here.
• ChemSpider
It is a very similar database to Pubchem but with fewer chemicals. It
might be a good addition to use it with PubChem if you are planning
to do something big. The link is here.
26. MOLECULES DATASETS
• ChEMBL
It is a manually curated dataset for bioactive molecules with drug-like
properties. Currently, it contains 2M compounds and 1.1M assays.
Additionally, they use data mining to gather more data about molecules
(e.g. from patent documents). https://www.ebi.ac.uk/chembl/
• ZINC
A free database of commercially-available compounds for virtual screening.
https://zinc.docking.org/
27. MOLECULAR GRAPHICS VISUALIZATION TOOLS
• RasMol
One free molecular graphics visualization tool available over the Internet is
RasMol, developed by Roger Sayle. RasMol is available for UNIX, VMS, Macintosh
and Microsoft Windows (OS/2 and Windows NT).
• Chime
An alternative free visualization tool is the Netscape (TM) 3.01 Plugin called
Chime, supplied by: MDL Information Systems
28. MOLECULAR GRAPHICS VISUALIZATION TOOLS
• WebLab(TM) Viewer
A third free visualization tool is WebLab(TM) Viewer, provided by:
Molecular Simulations
• DisMol applet
A fourth free visualization tool is DisMol, created by Peter McCluskey
29. SOFTWARE FOR MOLECULAR PROPERTIES
• Molsoft
Molecular property prediction and Drug Likess property
• Molinspiration ( http://www.molinspiration.com )
It offers broad range of cheminformatics software
tools supporting molecule manipulation and processing,
including SMILES and SD file conversion, normalization of
molecules, generation of tautomer's, molecule fragmentation,
calculation of various molecular properties needed in QSAR,
molecular modelling and drug design
30. SOFTWARE FOR MOLECULAR PROPERTIES
• OSIRIS Property Explorer ( http://www.organic-chemistry.org/prog/peo/)
To predict mutagenic, tumorigenic, irritant, reproductive effect, Drug likeness and
Drug Score.
• ALOGPS
cheminformatics tasks including the building and visualisation of chemical
structures, the calculation of molecular properties and the analysis of relationships
between chemical structure and properties
http://www.vcclab.org/lab/
31. DOCKING SOFTWARE
• Auto Dock
• Auto Dock Vina
• Argus Lab
• HEX
• SwissDock
• DINC Web Server
• MTiAutoDock
• Pyrx
• NP Dock
• GEMDOCK
• EADOCK
• Schrödinger
32. FREE BOOK WEBSITE
These are the top sites where you can
download e-materials for free:
1. www.pdfdrive.net
2. www.b-ok.org
3. www.4shared.com
4. www.bookboon.com
5. www.worldreader.org
6. www.bookfi.net
7. www.christianbook.com
8. www.ebookee.org
9. www.sharebookfree.com
10. www.pink.monkey.com
11. www.obooko.com
12. www.manybooks.net
13. www.epubbud.com
14. www.bookyards.com
15. www.getfreeebooks.com
16. www.freecomputerbooks.com
17. www.essays.se
18. www.sparknotes.com
33. REFERENCES
• Satish A Bhalerao, Deepa R Verma, Rohan L D’souza, Nikhil C Teli, and Vinodkumar S
Didwana. Chemoinformatics: The Application of Informatics Methods to Solve
Chemical Problems. RJPBCS 2013 : 4 (3); 475 -499
• B.Firdaus Begama and Dr. J.Satheesh Kumarb. A Study on Cheminformatics and its
Applications on Modern Drug Discovery. Procedia Engineering 2012: 38; 1264 – 1275.
• Chemoinformatics – A textbook. J. Gasteiger & T. Engel (eds). Wiley-VCH, 2003.
• https://www.rcsb.org/
