Protocols / Techniques Covered

Topic	Contents	Tools
Bioinformatics
Bioinformatics - An Overview	Definition and History Information Networks Internet in Bioinformatics. Classification of amino Acids, Classification and three Dimensional structures of proteins. Overview of protein structure, Ramachandran Plot, Protein purification, Post translation modification, Protein trafficking.
Databases	Protein Information Resources: Biological Databases, Primary Sequence, Composite Protein Sequence Databases, Secondary Databases Prosite, Prints Blocks Profiles and Identity. Genome Information Resources: DNA sequence Databases - EMBL DDBJ Genbank GSDB (Genome Sequence Database). Protein Data bank (PDB), Nucleic Acid Data Bank (NDB), Molecular modeling Data Bank (MMDB), Uniprot, Prosite, SCOP, CATH, BLAST, FASTA, Clusatl, Prodom.
Gene Prediction & Functional Aaalysis	Primer designing, ESTs and Gene discovery, Restriction site detection
Matrix, Fold Recognition & Sequence Analysis	Pairewise sequence comparison- sequence queries against biological databases	BLAST and FASTA multifunctional tools for analysis
	Pair wise sequence alignment, gaps, gap- penalties, scoring matrices, PAM250, BLOSUM62, local and global sequence alignment, multiple sequence alignment.	ClustalW, BLASTp
Secondary Structure Prediction	Propensity value.
Protein Structure Prediction	Homology modeling and Threading. Prediction of protein structure from sequences, functional sites	Modeller, PROSEARCH, Protoparm
Binding Site Analysis	Model evaluation, and Model validation	CASTp
Phylogenetic Analysis	Evolution, elements of phylogeny, methods of phylogenetic analysis, Phylogenetic tree of life, comparison of genetic sequence of organisms	Phylip, ClustalW
Genetic Algorithm	Algorithms in bioinformatics
Docking of Small Molecules		Autodock, Vina, igemdock
Drug Discovery & Computer Aided Drug Designing	Introduction, drug discovery area, pharmacogenetics and pharmacogenomics applications, SNPs, parameters in drug discovery identification of drug target molecules, drug design and its approaches, computer-aided drug designing methods; computer aided molecular design (CAMD), structure- based drug design, De novo design.
Recent advances in Drug design methodologies	Structure activity relationship
Virtual Screening	Structure based pharmacophore. Screening of various chemical databases	Zinc database
Immunoinformatics
Introduction to Immunoinformatics & Immunological Databases	dbMHC-MHC database at NCBI, T-cell epitope databases, B-cell epitope databases. SYFPEITHI MHC-presented epitopes
Homology modelling of antibody		Phyre 2, Modeller
Prediction of Cytotoxic T Cell (MHC Class I) Epitopes	Antigen Processing in the MHC ClassI Pathway	NetCTL, SYFPEITHI, CTL Pred, NetMHC server
MHC-II Prediction - Prediction of Helper T Cell (MHC Class II) Epitopes	Processing of MHC Class II Epitopes	HLApred, MHC2Pref, Propred
B Cell Epitope Prediction & Web Sources	Recognition of Antigen by B Cells- vaccine design- Web-Based Tools for Vaccine Design	PEPVAC, SVRMHC, NetCTL, BIMAS etc

Durations & Topics:

5 Days Duration: Headings 1, 2, 14, 15 & 16 + A Minor Online Project (Optional)

10 Days Duration: Topics 1, 2, 3, 4, 5, 6, 14, 15, & 16 + A Minor Online Project (Optional)

20 Days Duration: Topics 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15 &16 + A Major Online Project (Optional)

1 Month Duration: Topics 1 to 16 + A Major Online Project (Optional)

45 Days Duration: All the topics mentioned above + An Online Publication Project (Optional)

Fee Structures for Immuno Informatics Course Finishers Training