Unit 1

Lectures 12

Introduction to Concept of Genomics, Proteomics and Bioinformatics; Databases on web: Genome, Proteome and Molecular biology; Sequence alignment: Near-optimal sequence alignment; Global pair wise sequence alignment; Multiple sequence alignment; Genome rearrangement; Evolutionary Bioinformatics: Phylogenetic tree construction and analysis. Different methods used for protein evolution; Protein Modeling: Protein structure prediction and analysis, 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 3D molecular structures, Chemical databases and its implications, Pharmacophore model, Virtual screening, Ligand based and structure-based molecular design; Commands and Languages: Basic Unix and Linux commands, Extensible markup language and its use in Bioinformatics; Sequence similarity and database search: Pattern recognition and matching; Quantitative and probabilistic
pattern matching; Sequence pattern databases, Spectral pattern matching, String matching algorithm.

Unit 3

Lectures 6

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

Unit 4

Lectures 15

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

Pre-requisites: Basic understanding of computer and biology

Total number of classes: 45

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)

PSO 1 – Biochemical organization and cellular complexity in function

PSO 2 – Biomolecules in Medicine

PSO 3 – Molecular dysregulation in diseases

PSO 4 – Molecular technology in diagnosis and therapy

PSO 5 – Cell based approaches in diagnosis and therapy

PSO 6 – Microorganisms in Medicine

PSO 7 – Nanoscale entities and its significance in Medicine

PSO 8 – Tissue architecture engineering in Medicine

PSO 9 – Compounds as drugs and its efficacy

PSO 10 – Bioinformatics and biological data use

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.