Course

Unit 1

Introduction to Bioinformatics – applications of Bioinformatics – challenges and opportunities – introduction to NCBI data model- Various file formats for biological sequences. Bioinformatics resources Importance of databases – Biological databases- Primary & Secondary databases. Sequence alignment methods- pairwise sequence alignment methods- Use of scoring matrices and gap penalties in sequence alignments- PAM and BLOSUM Scoring Matrices. Introduction to Dynamic Programming, Global alignments: Needleman Wunsch Algorithm, Local Alignments: Smith Waterman Algorithm, Gap Penalties. Multiple sequence alignment methods Tools and application of multiple sequence alignment.

Unit 2

Sequence alignment tools, Phylogenetic analysis algorithms:Cladistic, and Phenetic methods- Clustering methods – Rooted and Unrooted tree representation Maximum Parsimony, UPGMA. Gene Prediction methods and tools – similarity based and ab-initio prediction- Protein Domain analysis – Pfam, MOTIF search. Structure prediction methods: Chou-Fasman, GOR method, Neural Network, Threading and Fold recognition. Principles of protein folding. Types of interaction between atoms – Bond distance, Bond angle, Torsion Angle, Bond energy and Dipole- Dipole interactions. Methods to study protein folding – phi, psi & omega angles with distance. Zwitterion, Disulfide Bridge and Ramachandran Plot. Types of Helices, Beta turns, Gamma turns. FSSP, VAST and DALI.ProteinMis-folding and aggregation.

Unit 3

Introduction to pharmacogenomics, pharmacodynamics, pharmacokinetics and toxicogenomics. Process of drug development-clinical trials phases- Routes of drug administration – Biotransformation (Metabolism) of drugs and related organic compounds – Historical Development of QSAR, Tools and Techniques of QSAR, Molecular Structure Descriptors. Multivariate Statistical methods in QSAR, Important Drug Databases, General pathways, sites of drug biotransformation, factors affecting drug metabolism and variability in drug response-ADME properties-physiological factors related to drug absorption and drug distribution. Designing Lipinski’s Rule of Five, ADMET screening, Docking Studies.

Text Books / References

References/ Textbooks

1. Higgins,Des and Taylor Williw: Bioinformatics: Sequence , Structure and databanks, Oxford , University Press,2000.
2. Baxenvants, AD., Bioinformatics: A practical guide to the analysis of genes and proteins”, Third edition, John wiley&      Sons ,2005
3. Teresa Attwood, Introduction ToBioinformatics,Pearson Education Singapore Pte Ltd, 2007
4. Mount, DW, Bioinformatics: Sequence and Genome analysis”, Second edition, Cold Spring Harbor Laboratory Press. Baxevanis
5. A.D., Davison D.B., Page R. D. M. & Petsko G.A. Current Protocols in Bioinformatics. New York, John Wiley &       Sons Inc., 2004
6. S.C. Rastogi et al, Bioinformatics: Methods and Applications: (Genomics, Proteomics and Drug Discovery) Kindle Edition.
7. Leach Andrew R., Valerie J. Gillet, An introduction to Chemoinformatics. Publisher: Kluwer academic, 2003. ISBN: 1402013477.
8. Gasteiger Johann, Handbook of Chemoinformatics: From Data to Knowledge, 2003. Publisher: Wiley-VCH. ISBN:3527306803.
9. Opera Tudor I,Ed. , Chemoinformatics in drug discovery, Wiley-VCH Verlag,2005
10. Kenneth M Merz, Jr, Dagmar Ringe, Charles H. Reynolds, Drug design: Structure and ligandbased approaches (2010) publisher: Cmabridge University press 

Course Outcomes

• CO1: Apply pairwise and multiple sequence alignment to the biological databases.
• CO2: Apply UPGMA and clustering methods for sequence alignment. Also gain knowledge in protein structure prediction
• CO3: Understand the concept of   quantitative structure and activity relationship and ADME properties related to drug metabolism

CO-PO Mapping