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Introduction

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10 views19 pages

Introduction

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pavithirasrias
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© © All Rights Reserved
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Cheminformatics

and Applications
Chemical Space: Small Molecules in Organic
Chemistry

Understanding chemical space


Small molecules:
chemical synthesis
drug design
 chemical genomics,
systems biology
 nanotechnology
And others
2
Cost to develop and time to market of various products

3
What is Cheminformatics?
• It encompasses the design, creation,
organisation, management, retrieval, analysis,
dissemination, visualization and use of chemical
information
• It is the mixing of information resources to
transform data into information and information
into knowledge, for the intended purpose of
making better decisions faster in the arena of
drug lead identification and optimization
What is Cheminformatics?
• “the set of computer algorithms and tools
to store and analyse chemical data in the
context of drug discovery and design
projects”
• Cheminformatics is the application of
informatics methods to solve chemical
problems
Resources
Books:
J. Gasteiger, T. E. and Engel, T. (Editors) (2003).
Chemoinformatics: A Textbook. Wiley.
A.R. Leach and V. J. Gillet (2005). An Introduction to
Chemoinformatics. Springer.
Journal:
Journal of Chemical Information and Modeling
Web:
http://cdb.ics.uci.edu
and many more………
Why We Need Chemoinformatics?

1) An enormous amount of data and maintenance of data

2) Can we gain enough knowledge from the known data to make


predictions for those cases where the required information is
not available?

3) Relationships between the structure of a compound and its


biological activity, or for the influence of reaction conditions
on chemical reactivity.
The Scope of Chemoinformatics

Representations and Structure Searching

Substructure Searching

Similarity Searching, Clustering, and Diversity Analysis

Searching Databases

Computer-aided Structure Elucidation

3D Substructure Searching

QSAR and Docking


Kinds of chemistry databases
• Small-molecule databases
– Databases of commercially-available compounds (e.g. ACD,
http://www.mdl.com/products/experiment/available_chem_dir/index.jsp)
– Proprietary chemical structure databases
– Literature databases
– Patent databases
– Small project-specific databases
• Protein databases
– Public, online databases (e.g. PDB, http://www.pdb.org)
– Proprietary and project-specific databases
Software Companies
Accelrys -Large chemoinformatics company
ACD/Labs - analytical informatics & predictions
BCI - 2D fingerprinting, clustering toolkits & software
Bioreason - HTS data analysis software
Cambridgesoft - 2D drawing tools & E-notebooks
CAS - produce Scifinder Scholar searching software
ChemAxon - Java based toolkits and software
Daylight- 2D representation & searching software
Leadscope - 2D structure and property tools
Lion Bioscience - produce LeadNavigator
MDL - Large chemoinformatics company
Openeye - Fast 3D docking, structure generation, toolkits
Quantum Pharmaceuticals - prediction, docking, screening
Sage Informatics - ChemTK 2D analysis software
Tripos-Large chemoinformatics company
2D searching with Oracle chemistry cartridges

Daylight DayCart – http://www.daylight.com/products/daycart.html


• Tripos Auspyx –
ttp://www.tripos.com/sciTech/inSilicoDisc/chemInfo/auspyx.html
• Accelrys Accord for Oracle –
http://www.accelrys.com/accord/oracle.html
• MDL Relational Chemistry Server –
http://www.mdl.com/products/isisdirect.html
• IDBS ActivityBase – http://www.id-bs.com/products/abase/
• Chemaxon JChem Cartridge – http://www.jchem.com
3D Structure generation and minimization

Concord from Tripos, Inc. One of the first 3D structure generation


programs, and is still being refined and developed. It generates single,
minimal-energy structures from input 2D structures. The program can
input and output a variety of file formats.
http://www.tripos.com/sciTech/inSilicoDisc/chemInfo/concord.html
Corina from the Gasteiger group. It is similar to Concord.
http://www2.chemie.uni-erlangen.de/software/corina/free_struct.html
Omega from OpenEye is the latest release. It offers very fast generation
of multiple low-energy conformers.
http://www.eyesopen.com/products/applications/omega.html
Depiction Tools for 3D structures
MDL Chime is a web browser plug-in that allows 2D and 3D structures to be
viewed in web pages. It can be used to visualize both proteins and small
molecules, and includes some limited ability to create molecular surfaces. It
is excellent for communicating structures via the web and for use in writing
web-based chemoinformatics software. http://www.mdlchime.com

ArgusLab is a free molecular modeling program that has a fairly extensive


set of options for 3D visualization, calculation of surfaces and properties,
minimization, and molecular docking. http://www.arguslab.com.
Chemistry Based Data Mining And Exploration

Structure
Data bases
searchable
Chemical(s) Chemical Structural Property Biological or
of concern Specific analogue analogue mechanistic
data analogue
Data mining Structure activity relationships
Applications of Chemoinformatics

1. Chemical Information

 Storage and retrieval of chemical structures and associated


data to manage the flood of data

 Dissemination of data on the internet

 Cross-linking of data to information

2. All fields of chemistry

• Prediction of the physical, chemical, or biological properties


of compounds

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3. Bioactive molecules

• identification of new lead structures

• optimization of lead structures

• establishment of quantitative structure-activity relationships

• comparison of chemical libraries

• definition and analysis of structural diversity

•planning of chemical libraries

16
Contd……
analysis of high-throughput data

docking of a ligand into a receptor

prediction of the metabolism of xenobiotics

analysis of biochemical pathways

4. Organic Chemistry

Prediction of the course and products of organic reactions

Design of organic synthesis

17
5. Analytical Chemistry

• Analysis of data from analytical chemistry to make predictions on


the quality, origin, and age of the investigated objects

• Elucidation of the structure of a compound based on spectroscopic


data

Teaching Chemoinformatics

 Chemists have to become more efficient in planning their


experiments, have to extract more knowledge from their
data

18
SAR Application

Maximum activity Prediction of toxicity

DRUG DESIGN ENVIRONMENTAL PROTECTION

Minimize toxicity

•Single therapeutic target •Multiple unknown targets


•Drug like chemical •Diverse Structures
•Some toxicity anticipated •Human and ecosystems

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