Certificate Programme in Bioinformatics

PAPER - I
BIOPHYSICS AND STRUCTURAL BIOLOGY
UNIT - I
Bioinformatics - an overview, Definition & History - Internet resources - Cell
structure and function - cell organelles - Key Biomolecules - lipids,
polysaccharides, proteins, nucleic acids - overview of protein and nucleic acid
structure
UNIT - II
Proteins - Amino acids - Peptide bond - Ramachandran map - Protein
denaturation and renaturation - Levels of protein structure - \u0001-helix, *-sheet and *-
turns - Super secondary structures - Domains - quaternary structure -DNA and
RNA structure - helical structures of DNA - Watson and Crick model - A, B and Z
forms of DNA - RNA secondary structure - different forms of RNA
UNIT - III
Methods for structure determination - Spectroscopic techniques - Infrared (IR),
Ultraviolet (UV)-Visible spectroscopy - Fluorescence spectroscopy - Nuclear
Magnetic Resonance (NMR) techniques - application to bio-macromolecules - Xray
crystallographic method of structure determination - Phase problem - Electron
density map and interpretation - structure refinement.
UNIT - IV
Methods of structure prediction - secondary structure prediction methods - Chou-
Fasman, GOR - tertiary structure prediction - Homology (comparative) modeling -
Fold recognition (threading) - ab initio method - Monte Carlo - Rosetta - CASP
UNIT - V
Genetic Engineering - DNA sequencing - Introduction to human genome project -
Genomics & Proteomics - Protein engineering - Structure-based drug discovery -
binding sites detection - docking.
PAPER - II
COMPUTATIONAL METHODS IN BIOINFORMATICS
UNIT - I
DNA & Protein Sequence analysis - Pairwise sequence comparison - Sequence
databases and searches - Swiss-Prot, NBRF-PIR, GenBank, DDJB - BLAST and
FASTA search.
UNIT II
Algorithms for pairwise sequence alignment - Scoring matrices - PAM and
BLOSUM - Local and Global alignment concepts - dynamic programming
methodology - Needleman and Wunsch algorithm - Smith-Waterman algorithm -
Statistics of alignment score - Multiple sequence alignments - Phylogenetic trees -
Profiles and motifs - distance and similarity - Evolutionary basis of sequence
alignment.
UNIT III
Protein structure data base (PDB) - Protein structure visualization tools - RasMol,
Swiss PDB Viewer - Structure - Classification, alignment and analysis - SCOP,
CATH, FSSP databases - Solvent accessibility and Interactions - Physicochemical
properties - Homology modeling using SPDBViewer or Insight II.
UNIT IV
Predicting Protein structure and function from sequence - Feature detection -
Domains & Motifs - BLOCKS, PRINTS, PFAM - Secondary structure prediction
- algorithms for predicting protein folds - Predicting 3D structure - comparative
(homology) modeling.
UNIT V
Genomics and Proteomics - Sequencing genomes - Sequence assembly - Genome
databases on the web (GDB) - Annotating and analyzing genome sequences -
Proteomics.
PAPER - III
BIOINFORMATICS AND COMPUTATIONAL BIOLOGY LAB
1. Study of Internet resources in Bioinformatics. E.g. NCBI, CGEB, EMBL.
2. Searches on MEDLINE, PubMed and CDROM bibliographic databases.
Concept of boolean operators in searching.
3. Introduction to sequence data bases
Protein sequence databank, NBRF-PIR, SWISSPROT, EMBL.
Nucleic acid sequence databank - Gene bank, EMBL
4. Pair wise alignment- Needleman-Wunsch and Smith-Waterman algorithms
5. Multiple alignment- CLUSTALW & PRINTS
6. BLAST, FASTA programs for sequence database search
7. Genome data bank - study the features of human genome.
8. Evaluation of protein structure by Swiss PDB viewer and by other molecular
visualization tools.
9. Calculation of phi - psi angles - Ramachandran plot.
10. Homology modeling of a given protein sequence.