Back close

Course Detail

Course Name Bioinformatics and Structure Based Drug Design
Course Code 25CLG532
Program M. Sc. Clinical Genomics
Semester 1
Credits 3
Campus Kochi

Syllabus

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.

Introduction

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

Objectives and Outcomes

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.

CO–PO Mapping Table:

COs

PO1

PO2

PO3

PO4

PO5

PO6

PO7

PO8

PO9

PO10

PO11

PO12

CO1

3

2

1

2

2

CO2

3

3

2

3

3

1

2

CO3

3

3

3

3

3

1

1

2

CO4

3

3

3

3

3

3

CO5

3

2

2

2

3

1

1

2

Program Specific Outcomes (PSO):

PSO1. Apply fundamental molecular biology principles to interpret clinical genomic data.

PSO2. Use molecular techniques (e.g., PCR, RT-PCR, sequencing) to detect genetic mutations and biomarkers.

PSO3. Analyze genotype-phenotype correlations in inherited and acquired disorders.

PSO4. Identify pathogenic variants from NGS data and interpret their clinical relevance.

PSO5. Correlate molecular pathways with disease mechanisms and therapeutic targets.

PSO6. Develop and validate diagnostic assays based on molecular biology principles.

PSO7. Utilize molecular biology to support pharmacogenomic profiling and therapy optimization.

PSO8. Integrate multi-omic data (genomic, transcriptomic, epigenomic) for personalized health solutions.

PSO9. Apply molecular knowledge to cancer genomics, infectious diseases, and rare genetic disorders.

PSO10. Translate molecular discoveries into clinical interventions through evidence-based practice.

CO–PSO Mapping Table:

COs

PSO1

PSO2

PSO3

PSO4

PSO5

PSO6

PSO7

PSO8

PSO9

PSO10

CO1

2

1

CO2

3

2

1

2

CO3

2

2

3

2

2

CO4

3

2

2

2

CO5

2

2

 

Evaluation Pattern

Evaluation Pattern: 50+50 = 100

Internal Assessment – 50% 
Periodical 1  Exam  20% 
Periodical 2  Exam  20% 
Continuous Assessment  Assignment/Test/Quiz 10% 
50%
End Semester Examination- 50% 
Theory Exam  50% 
50%
Total 100%

Textbook/ References

Textbook:

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

Reference:

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

DISCLAIMER: The appearance of external links on this web site does not constitute endorsement by the School of Biotechnology/Amrita Vishwa Vidyapeetham or the information, products or services contained therein. For other than authorized activities, the Amrita Vishwa Vidyapeetham does not exercise any editorial control over the information you may find at these locations. These links are provided consistent with the stated purpose of this web site.

Admissions Apply Now