This document provides an overview of the field of chemoinformatics. It defines chemoinformatics as the combination of chemistry and information technology used to process and analyze chemical data. The document discusses common representations of molecules including 1D, 2D, and 3D formats. It also outlines several common file formats used in chemoinformatics like Mol, SDF, and SMILES. Finally, it describes several important chemical databases, including PubChem, ChemBank, ChEMBL, and DrugBank, and gives examples of chemoinformatics applications such as virtual screening and QSAR modeling.

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