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Course Curriculum

Unit - 1 Introduction of Molecular Docking
1.1 Introduction to moleuclar docking 00:13:00
1.2 Understanding the structure of protein 00:07:00
1.3 Understanding the active site of a protein 00:08:00
1.4 Understanding the ligand structure 00:06:00
1.5 Protein ligand interactions 00:06:00
Unit - 2 From Conventional to Modern Drug Design
2.1 Drug design 00:14:00
2.2 Shift from traditional to computational biology 00:07:00
2.3 Computer aided design and drafting 00:14:00
2.4 Structure based drug design 00:15:00
2.5 Virtual screening 00:17:00
2.6 Structure based virtual screening 00:08:00
2.7 Work-flow of multi-stage drug designing 00:16:00
Unit - 3 Molecular Docking Technique
3.1 Workflow of molecular docking 00:14:00
3.2 Molecular docking theory 00:21:00
3.3 Ligand induced conformation 00:19:00
3.4 Ligand poses 00:08:00
3.5 Binding affinity 00:04:00
3.6 Molecular docking task 00:06:00
3.7 Molecular docking programs 00:07:00
Unit - 4 Types of docking
4.1 Types of biomolecular reactions 00:07:00
4.2 Protein ligand docking 00:19:00
4.3 Protein ligand docking example 00:05:00
4.4 Protein-Protein docking 00:20:00
4.5 Protein-Protein docking examples 00:26:00
4.6 Protein-Peptide docking 00:15:00
4.7 Protein-Peptide docking example 00:03:00
4.8 Protein-DNA docking 00:24:00
4.9 Protein-RNA docking 00:25:00
4.10 Example 00:04:00
4.11 HADDOCK 00:05:00
Unit - 5 Modes of Docking
5.1 Modes of molecular docking 00:05:00
5.2 Rigid docking 00:16:00
5.3 Illustration of rigid docking and its process 00:15:00
5.4 Shifting towards flexible mode of docking 00:14:00
5.5 Semi-Flexible docking 00:08:00
5.6 Flexible Ligand, Rigid Protein 00:06:00
5.7 Flexible docking – explanation 00:11:00
5.8 Flexible docking-concept 00:14:00
5.9 Flexibility of protein in drug discovery 00:08:00
5.10 Example 1- CABS Dock 00:13:00
5.11 Example 2 00:06:00
5.12 Challenges of protein ligand docking 00:07:00
5.13 Example 3 00:06:00
Unit - 6 Sampling Algorithms
6.1 Sampling algorithms – Introduction 00:03:00
6.2 Semi-flexible docking- types 00:04:00
6.3 Systematic search techniques 00:14:00
6.4 Fragmentation search 00:14:00
6.5 Conformational Ensemble 00:17:00
6.6 Monte Carlo method 00:13:00
6.7 Genetic algorithms 00:21:00
6.8 Tabu search method 00:08:00
6.9 Swarm optimization method 00:06:00
6.10 Simulation method- molecular dynamics (example) 00:21:00
6.11 Sampling Algorithms for flexible docking 00:10:00
6.12 Soft Docking (examples) 00:15:00
6.13 Side chain flexibility 00:17:00
6.14 Multiple protein conformations 00:00:16
6.15 Average grid method 00:05:00
6.16 United description of the protein 00:13:00
6.17 Individual conformations 00:15:00
Unit - 7 Pose Selection
7.1 Pose selection (scoring functions) 00:13:00
7.2 Scoring function components 00:09:00
7.3 Classification of scoring function 00:21:00
7.4 Empirical scoring fuctions 00:12:00
7.5 Descriptors used in empirical scoring function 00:23:00
7.6 Knowledge based scoring fuctions 00:17:00
7.7 Evaluation scoring functions 00:12:00
7.8 Databases for evaluating scoring functions 00:14:00
7.19 Practical Session 1 01:00:00
Unit - 8 Docking Target
8.1 Understanding the structure file format- introduction 00:18:00
8.2 Types of records in PDB 00:10:00
8.3 Practical Session 2 01:00:00
8.4 Docking target – handling the protein structure 00:28:00
8.5 Prediction of active site & missing residues 00:15:00
8.6 Practical Session 3- Prediction of active site & modeling missing residues 00:49:00
8.7 Practical Session 4-Molecular Visualization Tool- Chimera 00:01:00
Unit - 9 Target Preparation
9.1 Selecting the traget molecule 00:26:00
Practical Session – 5 00:15:00
9.3 Practical session – 6 UniProtDB for receptor protein 00:28:00
Unit - 10 Retreiving Ligand Molecules
10.1 Practical Session 7 00:10:00
10.2 Practical Session – 8 PubChem 01:00:00
Unit - 11 Autodock
AutoDoc Practical Session – 9 02:00:00
Unit - 12 Preparing the Protein
12.1 Preparing the Protein – Practical Session 10 01:00:00
12.2 Generating the grid parameter file – Practical Session 12 00:50:00
12.3 Ligand molecule preparation – Practical Session 13 00:30:00
12.4 Docking – Practical Session 14 00:51:00
12.5 Analysis – Practical Session 15 00:53:00
12.6 Analysis of the docked complex – Practical Session 16 00:55:00
12.7 Molecular docking softwares 01:00:00
Unit 13 Applications
Applications of Molecular Docking 00:01:00
  • 4,500.00
  • 2 months
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