PI-610: Pharmacoinformatics-Bioinformatics		(2 credits)
1.	Bioinformatics basics: Computers in biology and medicine, Information Chaos, Challenges in post genomic era, Database concept, Protein and nucleic acid databases, specialized genome databases (HGD, MGD, SGD, TIGR, and ACeDB).
2.	Databases and search tools: Structural databases, Gene databases, Protein databases, Searching databases, The NCBI; Publicly available tools, Resources at EBI, Resources on the web; Database mining tools, Alphafold.
3.	Protein folding: Diversity in proteins function and protein structure, Link between sequence, structure and function, Misfolding problem, Anfinsen's dogma, Lavinthal's paradox, Challenges in understanding structure, Methods for determining 3D structure, Protein data bank, Visualization of macromolecules.
4.	Protein Flexibility: Dynamic motion in biological processes, Motion and function, Examples, Types of molecular motions, Time scale of protein motion, Methods to study protein motion, Data base of macromolecules, Online servers and software tools.
5.	Molecular recognition: Process of recognition, Complementary features upon binding, Tolerance upon binding, Induced fit theory, Adaptation of enzyme and ligand, Domino effect, Ensemble of conformations, Forces involved in recognition, Solvent effect, Hydrophobic effect.
6.	Secondary and tertiary structure of proteins: Protein architecture, Conformation, Ramachandran plot, Characteristics of secondary structural elements, Alpha helices, Beta sheet and reverse turns, Super secondary structure, Domains, New levels of protein architecture.
7.	Classification of protein folds and topology: All alpha topology, All beta topology, Alpha-beta topology, Alpha + beta topology, Classification of proteins, CATH, SCOP.
8.	Sequence Alignment: DNA/protein sequences analysis, Alignment, pairwise and global alignment, Multiple alignment, structure based alignment, software tools, BLAST, FASTA, CLUSTAL, Scoring matrices, Algorithms, Needleman-Wunsch and Smith-Waterman algorithms, Dynamics programming, Molecular Phylogenetics.
9.	Structure prediction of proteins: Homology modeling, Template selection, Sequence alignment, Secondary structure prediction methods, Online servers and software, Protein main chain and side chain modeling, Loop modeling, Tweak Algorithm, Refinement and evaluation of models, Structure prediction of GPCRs, Fold recognition methods, Ab initio method for structure prediction, software used for 3D structure prediction Structural genomics and its application.
10.	Applications of bioinformatics: Proteins history, Proteins and pharmaceutical industries, Disease areas, Complex proteins, Applications, structure based drug design.