Cheminformatics

The course comprises of following eight papers:

Paper 1 - Basics of Cheminformatics

• Introduction to Cheminformatics
• Evolution of Cheminformatics
• History of Chemical Information Science
• Use of Cheminformatics
• Prospects of Cheminformatics
• Cheminformatics Glossary

Paper 2 - Medicinal Chemistry - Receptor Ligand Interaction

• Introduction
• Drugs
• Classification of Drugs
• Medicinal Chemistry
• History of Medicinal Chemistry
• Drug Discovery
• Natural Sources of Lead Compounds
• Target Oriented Drug Design
• Drug Solubility

Paper 3 - Modern Combinatorial Chemistry

• Introduction: Concepts and Terms
• Solid-phase Strategies
• General Strategy and Concepts
• Specific Implementation Issues
• Chemical International Resources
• Specific Implementation Issues
• Anchoring Chemistry
• Coupling chemistry
• Protection Schemes
• Analytical Methods
• Solution Phase Strategies
• High Throughput Screening
• Design of Combinatorial Libraries
• Glossary of Combinatorial Chemistry Terms

Paper 4 - Cheminformatics Database Design & their Management

• Database Concept
• Database Architecture
• Codd Rules
• Normalization
• Access 2000 Database
• Accord 2000 Cheminformatics Database
• Introduction to Structured Query Language (SQL)
• Data Manipulation Language
• Data Definition Language
• SQL Reserved Words Overview
• SQL Commands Comparison for Access, Oracle and SQL Server
• Chemical Database Design & their Tools
• Structured based Searches

Paper 5 - Chemical Information Sources

• History and Future of the Scientific Internet
• Chemical Literature
• Types of Publication
• Journal/Technical Report/ Patents/ Conference/ Paper/ Dessertations/ Electronic Publications
• Chemical Information Searches
• Advantages/Limitation of Computer Searching
• Strategics and Tactics for Searchers
• Patent Searching Techniques, Patent Search at a Patent and Trademark Depository Library
• Computer Searching of Chemical Abstracts
• Substructure Searching in Chemical Abstracts
• Keyword-based General Bibliographic Searches
• Chemical connectivity and Structure Searches (2-D)
• Chemical Structure, Property and Shape Based Searches (3-D)
• Searching for the Synthesis or Reactions of Specific Compounds or Classes of Compounds
• Communication in Chemistry
• Chemistry in Newsgroups and Discussion Lists
• Molecular visualization Tools and Sites
• The Publication Process: Primary, Secondary and Tertiary Sources
• Analytical Chemistry
• Physical Property Information
• Chemical Safety and Toxicology Information
• Chemical History, Biography, Directories and Industry Sources
• Chemical Information Sources
• Guides to Chemical Information Sources and Databases

Paper 6 - Computational Chemistry

• Introduction
• Building Molecules
• Conformation Searching
• Molecular Dynamics
• Introductory Quantum Chemistry
• Basic Principles
• Extended Huckel Theory and Photoelectron Spectroscopy
• Symmetry and Z-matrix
• Ab initio Hartree-Fock Theory, basis sets closed and open-shell molecules
• Geometry optimization, Transition Structure optimization, Potential energy surface
• Semiempirical Methods, ZDO, CNDO, INDO, MNDO/AM1/PM3, Parameterization and performance
• Molecular Mechanics and force fields
• Force fields, Potential energy functions, inter and intramolecular interactions, Empirical parameters
• Molecular mechanics calculation, energy minimization, conformational
• Analysis vibrational frequencies and normal mode analysis
• Condensed Phase Modeling
• Debye-Huckel Theory, continuum solvation models (classical and SCRF)
• Explicit simulations methods, Monte Carlo, Molecular Dynamics, Brownian Dynamics
• Free energy simulation methods and discussion of Applications
• Biopolymers
• • Protein Structure, PDB
  • Nucleic Acid Structure, DNA Sequence, Database, WWW
  • Energy minimization, molecular dynamics, enzyme active site and discussion of Applications
• Software & Hardware
• Insight / Discover
• MOPAC
• Databases
• Quanto

Paper 7 - Data Sequencing Mining and Visualization

• An Introduction to Data Mining
• What is Data Mining?
• How Data Mining Works?
• An Architecture for Data Mining
• Differences between Data Mining & Machine Learning
• Data Visualization
• Visualizing Data Mining Models
• Decision Tree
• Data Mining and Analytical Technology
• Comparing Different Models using Visualisation
• Software - Past and Present Developments

Paper 8 - Drug Design and Discovery

• Development of New Drugs
• Prodrugs and Soft Drugs
• Chemical and Physicochemical Parameters in Drug Design
• Design of Enzyme Inhibitors
• Drug Metabolism
• Molecular Modeling using Computers
• Structure Based Drug Designing
• Computation Techniques in Drug Design Process