Overview
The Structural Bioinformatics & Modelling course is aimed at those interested in learning homology modelling, molecular simulation, and docking of biological molecules. Structural biology enables the understanding of the working mechanisms of the molecular components involved in biological processes. The major goal of this course is to introduce students to methods and database resources used in macromolecular structure determination and the study of their interactions, and to develop a deeper understanding of the connection between structure and function in drug discovery and therapeutic targets of the disease. This knowledge is particularly valuable for agriculture, pharmacy, microbiology, and biotechnology students, as it opens new possibilities for precision medicine, sustainable agriculture, and innovative pharmaceutical solutions.
Our Trainers
Dr Jyoti Kant Choudhari
Assistant Professor, School of Bioscience, Sanjeev Agrawal Global Educational (SAGE) University, Bhopal
Dr Shikha Tiwari
Assistant Professor at Sanjeev Agrawal Global Educational (SAGE) University, Bhopal
Modules
Week 1: Fundamentals of Bioinformatics
Module 1: Introduction to Bioinformatics
Topics Covered:
- Scope and applications of bioinformatics.
- Overview of biological data (genomics, proteomics, transcriptomics).
- Introduction to bioinformatics databases (NCBI, EMBL-EBI, UniProt) and tools.
Learning Outcomes:
- Define the scope of bioinformatics and its interdisciplinary nature.
- Identify key types of biological data and their relevance.
- Navigate and retrieve data from major bioinformatics databases.
Tools/Platforms:
- NCBI, EMBL-EBI, UniProt
- PubMed, GeneCards
Assignment 01:
- Quiz on fundamental concepts.
- Retrieve gene/protein data using NCBI and UniProt.
Module 2: Sequence Analysis & Comparative Genomics
Topics Covered:
- Introduction to sequence databases and retrieval.
- BLAST: Basic Local Alignment Search Tool (BLAST I).
- Advanced comparative genomics (BLAST II) and interpreting results.
Learning Outcomes:
- Perform sequence similarity searches using BLAST.
- Analyze and interpret alignment results.
- Compare genomic data across species.
Tools/Platforms:
- NCBI BLAST, Ensembl Genome Browser, UCSC Genome Browser
Assignment 02:
- Hands-on sequence retrieval and similarity search using BLAST.
- Comparative analysis between gene orthologs.
Module 3: Sequence Alignment Techniques
Topics Covered:
- Theory behind sequence alignment (pairwise and multiple).
- Global vs. local alignment.
- Tools for multiple sequence alignment and phylogenetic analysis.
Learning Outcomes:
- Differentiate between alignment types and their applications.
- Execute multiple sequence alignment.
- Interpret phylogenetic trees.
Tools/Platforms:
- Clustal Omega, MUSCLE, MEGA X
Assignment 03:
- Perform multiple sequence alignment.
- Construct a basic phylogenetic tree.
Week 2: Protein Structure & Molecular Docking
Module 4: Protein Structure & Visualization
Topics Covered:
- Levels of protein structure.
- Exploration of protein structure databases (PDB, UniProt).
- Visualization of 3D structures.
- Basic principles of protein structure prediction.
Learning Outcomes:
- Describe protein structural organization.
- Retrieve protein structure data from PDB.
- Visualize and analyze 3D protein models.
Tools/Platforms:
- RCSB PDB, UniProt
- PyMOL, Chimera, Swiss-Model
Assignment 04:
- Download and visualize protein structures.
- Annotate secondary structure elements.
Module 5: Molecular Docking
Topics Covered:
- Principles of molecular docking and drug discovery.
- Protein-ligand interactions.
- Docking algorithms, scoring functions.
- Overview of docking pipelines.
Learning Outcomes:
- Explain the basics of molecular docking.
- Set up a docking experiment using open-source tools.
- Analyze docking scores and binding poses.
Tools/Platforms:
- AutoDock Vina, SwissDock
- PyRx, Discovery Studio Visualizer (Lite)
Assignment 05:
- Perform a basic docking of a ligand to a protein target.
- Submit a short report on binding interaction analysis.
Outcomes
- A foundational understanding of bioinformatics concepts and biological data types will be developed.
- Techniques for sequence retrieval, analysis, and comparative genomics will be demonstrated using standard bioinformatics tools.
- Sequence alignment strategies, including pairwise and multiple alignments, will be applied and interpreted in the context of genomic studies.
- Protein structures will be retrieved, analyzed, and visualized using appropriate structural biology databases and visualization tools.
- Basic molecular docking experiments will be conducted, and protein-ligand interactions will be evaluated using computational tools.
