Chemoinformatics and its applications

1. CHEMOINFORMATICS
Presented by
Miss. Rupali D. Salunkhe
PG Department of Bioinformatics,
WCBT, Solapur

2. CONTENTS
 Introduction
 Representation of molecules
 File formats
 Databases
 Applications
 References

3. INTRODUCTION
 Chemoinformatics is the combination of chemistry and
information technology, is required for the processing
and analysis of chemical data.
 Design, creation, organization, management, analysis,
visualization and use of chemical information.
 It is the application of informatics methods to solve
chemical problems.
 It is relevant to biologists because chemistry data are
important in many areas of molecular biology, e.g, in the
study of protein interactions.

4.  The term chemoinformatics was defined by F.K.
Brown in 1998.
 It combines the scientific working fields
of chemistry, computer science and information
science.
 For example in the areas of topology, chemical
graph theory, information retrieval and data
mining in the chemical space.
 It can also be applied to data analysis for various
industries like paper , pulp and dyes industries.

5. REPRESENTATION OF MOLECULES
 1D– computed/experimental global properties
 2D – the chemical structure diagram
 3D – atomic coordinate data

6. FILE FORMATS
 Mol format
 SDF format
 SMILES format

7. MOL FORMAT
 An MDL Molfile is a file format for holding information
about the atoms, bonds, connectivity and coordinates of
a molecule.
 The format was created by MDL Information Systems
(MDL) [Molecular Design Limited, Inc.].
 It is also supported by some computational software
such as Mathematica.
 The molfile consists of - Header information ,the
Connection Table (CT) containing atom information,
then bond connections and types.

8. SDF FORMAT
 SDF is one of a family of chemical-data file formats
developed by MDL.
 SDF stands for structure-data file.
 SDF files actually wrap the molfile (MDL Molfile) format.
 Multiple compounds are delimited by lines consisting of
four dollar signs ($$$$).
 A feature of the SDF format is its ability to include
associated data.

9. SMILES FORMAT
 The Simplified Molecular Input Line Entry Specification
(SMILES) is a line notation for molecules.
 SMILES strings include connectivity but do not include 2D
or 3D coordinates.
 Hydrogen atoms are not represented.
 Other atoms are represented by their element symbols C,
N,O, S, Cl, Br, and I.
 The symbol "=" represents double bonds and "#"
represents triple bonds, branching is indicated by () and rings
are indicated by pairs of digits.

10. DATABASES
 PubChem
 ChemBank
 ChEMBL
 DrugBank

11. PUBCHEM DATABASE
 https://pubchem.ncbi.nlm.nih.gov/
 PubChem is a database of chemical molecules and their
activities against biological assays.
 Is maintained by the NCBI.
 It contains substance descriptions and small molecules
with more than 1000 atoms and 1000 bonds.
 Searching - chemical structure, name
fragments, chemical formula, molecular weight.

12. HOME PAGE OF PUBCHEM DATABASE

13. CHEMBANK DATABASE
 http://chembank.broadinstitute.org/
 It is a public, web-based informatics environment.
 Created by the Broad Institute’s Chemical Biology
Program.
 It stores information of small molecules and biomedically
relevant assays.
 It is intended to guide chemists synthesizing novel
compounds or libraries, to assist biologists searching for
small molecules.

14. HOME PAGE OF CHEMBANK DATABASE

15. CHEMBL DATABASE
 https://www.ebi.ac.uk/chembl/
 ChEMBLdb is a manually curated chemical
database of bioactive molecules.
 It is maintained by the European Bioinformatics
Institute (EBI), of the EMBL.
 ChEMBL database contains compound bioactivity
data against drug targets.
 The latest version 2 (ChEMBL_02).

16. HOME PAGE OF CHEMBL DATABASE

17. DRUGBANK DATABASE
 https://www.drugbank.ca/
 The DrugBank database is a comprehensive, freely
accessible, online database.
 Containing information on drugs and drug targets.
 It is widely used by the drug industry, medicinal
chemists, pharmacists, physicians, students.
 The latest release of the database (version 5.0.11).
 It contains 11,002 drug entries.

18. HOME PAGE OF DRUGBANK DATABASE

19. APPLICATIONS
 Storage and retrieval- The primary application is the
storage, indexing and search of information relating to
compounds.
 Virtual libraries- Chemical data can related to real or
virtual molecules,Virtual libraries of classes of
compounds: drugs, natural products, diversity-oriented
synthetic products.
 Virtual screening-It involves computationally screening in
silico libraries of compounds.
 Quantitative structure-activity relationship (QSAR)-Used
to predict the activity of compounds from their structures.

20. REFERENCES
 An introduction to cheminformatics, A. R. Leach, V. J.
Gillet.
 Cheminformatics, Johann Gasteiger and Thomas
Engel (Eds).
 Molecular modelling – Principles and Applications, A.
R. Leach.
 Gasteiger, Editor, Handbook of Chemoinformatics -
From Data to Knowledge, Wiley-VCH, Weinheim.

21. THANK YOU