Course

Unit 1

Lectures 12

Introduction to Concept of Genomics, Proteomics and Bioinformatics; Databases on web:Genome, Proteome and Molecular biology; Sequence alignment: Near-optimal sequencealignment; Global pair wise sequence alignment; Multiple sequence alignment; Genomerearrangement; Evolutionary Bioinformatics: Phylogenetic tree construction and analysis. Different methods used for protein evolution; Protein Modeling: Protein structure prediction andanalysis, Protein visualization software, Protein dynamics and Protein structure validation tools.

Unit 2

Lectures 12

Chemoinformatics: Basic idea of molecule design, Visualization and generation of 2D and 3Dmolecular structures, Chemical databases and its implications, Pharmacophore model, Virtualscreening, Ligand based and structure-based molecular design; Commands and Languages: BasicUnix and Linux commands, Extensible markup language and its use in Bioinformatics; Sequencesimilarity and database search: Pattern recognition and matching; Quantitative and probabilistic pattern matching; Sequence pattern databases, Spectral pattern matching, String matchingalgorithm.

Unit 3

Lectures 6

Machine learning, Deep learning and Artificial Intelligence in Drug discovery; Few case studiesof integrating this methodology towards in vitro/in vivo model systems in understanding themolecular basis of the disease.

Unit 4

Lectures 15

Lab course work:Basic linux commands and linux editors, X-windows and linux environment used for learningdifferent linux commands and text editors like vi, xedit etc. Exposure to different usefuldatabases, virtual screening and Data mining, Different biologically important databases wereexplored. Structural similarity search of drug like molecules were mined from different smallmolecular databases. Sequence alignment studies of protein family using BLAST software.

Pre-requisites: Basic understanding of computer and biology

Preamble: Compiling and articulating mammoth of biological information is the key to development of focused research and generation of theoretical models for predicting structure and function saving valuable research-time and efforts. This course will bring the students to conceptual understanding about the significance of bioinformatics as a whole and equip them to understand this molecular highway of information towards its effective use and development of therapy in medicine.

Total number of classes: 45

Course Outcome

CO1 Basic concepts on amino acids, peptide bond, Genomics basics, database analysis and structure-property relationships.

CO2 Pairwise and Multiple sequence alignment methods, algorithms and applications and understanding the sequence conservation for protein sequence-function relationships

CO3 Molecular docking, pharmacophore modeling, protein ligand complex interactions and its mechanism of action, QSAR, QSPR, QSTR techniques used in Chemoinformatics field.

CO4 Different techniques in Machine learning and deep learning, concepts taught to make awareness in molecular modeling studies. Its integration with wet lab studies will be discussed.

CO5 Skills working in Linux environment; Different linux commands and linux editor will be taught; Sequence alignment studies; Macromolecule sequence-structure and function studies and visualization using different software.

Program Specific Outcomes. (PSO)

PSO1. Demonstrate comprehensive knowledge of stem cell biology and their clinical and research relevance.

PSO2. Apply core laboratory techniques for stem cell isolation, characterization, and manipulation.

PSO3. Integrate principles of tissue engineering and biomaterials for regenerative applications.

PSO4. Analyze drug delivery, pharmacokinetics, and bioinformatics relevant to stem cell-based therapies.

PSO5. Evaluate ethical, regulatory, and translational aspects of stem cell product development.

PSO6. Bridge basic science with translational approaches in regenerative medicine and gene therapy.

PSO7. Design and interpret experimental strategies for stem cell-based disease

modeling and preclinical studies.

Evaluation Pattern: 50+50 = 100

Textbooks

1. Mount D W, “Bioinformatics Sequence and Genome Analysis”, Cbs Publishers & Distributors (2003), ISBN: 8123909985
2. Jenny G and Philip E B, “Structural Bioinformatics”, Second Edition, Wiley-Blackwell publisher (2011). ISBN: 978-1-118-21056-7
3. Practical Bioinformatics; Editors: Bujnicki, Janusz M. (Ed.), Series: Nucleic Acids and Molecular Biology, Springer publisher, 10.1007/978-3-540-74268-5, 2008.

References

• Mohan CG, “Structural Bioinformatics- Applications in Preclinical Drug Discovery Process”, Springer Nature Publisher, 2019. ISBN 978-3-030-05282-9.