Course Title: Bioinformatics Tools for Comparative Genomics and Protein

Interaction Modelling
Course Code: ENV3

Course Description:
This course to study application of bioinformatics software tools to analyse biological
processes on the levels from genome functioning to interaction of individual molecules.
Themajor focus of the course is on application of the commercial program Accelrys
Discovery Studio.
Graphical User Interface of the program will be explained in detail that will be followed
by practical tutorials on the use of the program to study molecular interactions, search
for targets for new antibiotics and assessment of affinities of multiple compounds to the
active sites of multiple known pharmacophores. Several other soft-ware tools used in
comparative genomics will be presented.

Who should attend?

This course is for undergraduates, postgraduate students and staff members interested in
modelling and analysis of biological process and particularly involved in new drug
design.

Course Content:
Day 1
Introduction to the Discovery Studio Client
Main principles and approaches;
Opening and editing a molecular structure;
Other useful techniques: creating charts and movies, scripting;

Day 2
Small Molecule tools tutorial
Working with ADMET;
Learn how to use the Search Small Molecule Conformations tool panel;
Learn how to select a diverse subset of ligands from a combinatorial library
and optimize that selection for diversity and some Lipinski properties;
Study a library of diverse ligands;
Day 3
Macromolecule tools tutorial
Search and analysis of homologous sequences;
Overview of functionality that enables you to gain insights into a structure's
function by looking at its sequence
Trans membrane protein modeling;
Protein docking;
Day 4
Receptor-Ligand Interaction tools
Learn the basic features of the 2D Window;
Learn how to find binding sites and define a search sphere;
Dock a set of ligands;
Perform a lead optimization;
Day 5
Pharmacophore tools
Optimize a scaffold in a protein active site using a fragment pharmacophore
method;
Use a training set of six active ligands to derive common feature
pharmacophores for lead identification;
Learn how to build a basic pharmacophore starting from a single
conformation of a ligand;

Day 6
Repetitions, practicals, introduction to scripts
Day 7
Introduction to BioPython, My SQL and use of BATCH in Windows
Basics of programming on Python;
Module BioPython to perform basic bioinformatics tasks;
Creation and use of My SQL databases;
Scripting for Windows;
Day 8
Phylogenetic analysis and metagenomics
Algorithms and types of phylogenetic trees;
Validation of phylogenetic trees;
Concepts of gene tree and species tree, gene tree reconsilidation;
Phylogenomics and metahenomics;
Local BLAST and the program Megan for analysis and visualization of
metagenomic datasets;
Day 9
Basic bioinformatics tools for comparative genomics
Sequence alignment and search through sequence databases;
Genome browsers;
Protein function prediction by homology;
Day 10
Introduction to SeqWord:
Compositional polymorphism of genomes;
Identification of genomic islands; and

Spare time for repetition and practical tasks

Course Period:
From 5 to 10 days.

Course Style:
Lecture or One-to-One training style.
In house training.
Group Training.
Practical Training.

Remember:
We provide this course in any place and at any time suitable for you.
This course is provided in VIP or standard forms. For more information
contact BATD team.

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