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Course Detail

Course Name Bioinformatics and Structure based drug design
Course Code 25NBT532
Program M. Sc. Nanobiotechnology (NBT)
Credits 3
Campus Kochi

Syllabus

Unit 1

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

Chemoinformatics: Basic idea of molecule design, Visualization and generation of 2D and 3Dmolecular structures, Chemical databases and its implications, Pharmacophore model, Virtual screening, Ligand based and structure-based molecular design; Commands and Languages: BasicUnix 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

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

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.

Objectives and Outcomes

Pre-requisites: Basic understanding of computer and biology

 

Total number of classes: 45

Course Outcome

  • Basic concepts on amino acids, peptide bond, Genomics basics, database analysis and structure-property relationships.
  • Pairwise and Multiple sequence alignment methods, algorithms and applications and understanding the sequence conservation for protein sequence-function relationships
  • Molecular docking, pharmacophore modeling, protein ligand complex interactions and its mechanism of action, QSAR, QSPR, QSTR techniques used in Chemoinformatics field.
  • 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.
  • 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.

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 Outcomes (PO) (As given by NBA and ABET)

PO1: Bioscience Knowledge

PO2: Problem Analysis

PO3: Design/Development of Solutions

PO4: Conduct Investigations of complex problems

PO5: Modern tools usage

PO6: Bioscientist and Society

PO7: Environment and Sustainability

PO8: Ethics

PO9: Individual & Team work

PO10: Communication

PO11: Project management & Finance

PO12: Lifelong learning

 

CO- PO MAPPING:

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PROGRAM SPECIFIC OUTCOMES (PSO):

 

PSO1: Mastery of Nanomaterial Science and Characterization

PSO2: Understanding of Cellular and Molecular Systems

PSO3: Application of Nanobiotech in Diagnostics and Therapy

PSO4: Experimental Design and Data Analysis

PSO5: Research Competency and Methodological Rigor

PSO6: Industry and Career Readiness

0 – No affinity; 1 – low affinity; 2 – Medium affinity; 3 – High affinity

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CO 5

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3

 

CO-PSO MAPPING:

Text Books / References

TEXT BOOKS:

  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.

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