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In Silico Techniques Summer Training Program

The document outlines a one-month summer training program focused on in silico techniques, covering topics such as protein structure, modeling, docking, and molecular dynamics. The program includes lectures and hands-on sessions scheduled three days a week, with specific modules for practical applications and project work. Participants will engage in presentations and receive certificates upon completion.

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saraattia
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14 views5 pages

In Silico Techniques Summer Training Program

The document outlines a one-month summer training program focused on in silico techniques, covering topics such as protein structure, modeling, docking, and molecular dynamics. The program includes lectures and hands-on sessions scheduled three days a week, with specific modules for practical applications and project work. Participants will engage in presentations and receive certificates upon completion.

Uploaded by

saraattia
Copyright
© All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd

Summer training program table

Duration: One Month | Schedule: Sunday, Tuesday, Thursday (3 Days/Week)

Week Day Session Title / Modules Time Activity Type


Module 1: Protein Structure & Function
Revision
- Amino acids, peptide bonds, primary to
quaternary structures
- Forces stabilizing structure (H-bonds,
hydrophobic, electrostatic)
- Protein folding and misfolding
- Free energy concepts in biological
Day 1
systems
(3-8-2025)
- PDB database Lecture +
10:00 AM –
Hands-on
3:00 PM
Module 2: Introduction to In Silico (PyMOL, VMD)
Methods
- Computational chemistry & bioinformatics
Week 1:
overview
Foundations of
- Installation of PyMOL, VMD and their
In Silico
basics
Techniques
Module 3: Protein Modeling I - Homology
Modeling
- Principles of homology modeling
- Sequence alignment and template Lecture +
Day 2 selection 10:00 AM –
Hands-on
(5-8-2025) - Software: SWISS-MODEL, AlphaFold 2 3:00 PM
(Online servers)
Week Day Session Title / Modules Time Activity Type

- Hands-on: Modeling a simple protein using


online servers

Module 4: Protein Modeling II -


Refinement & Validation
- Quality assessment
- Refinement of modelled structures
- Hands-on: Refining and validating
modeled structures

Module 5: Chemical Compound


Modeling & Minimization
- Small molecule structures (2D/3D)
- Different file formats and their conversion
using OpenBabel (SDF, PDBQT, Mol2) Lecture +
Day 3 - Minimization and conformational analysis 10:00 AM – Hands-on
(7-8-2025) using OpenBabel and Avogadro 3:00 PM (OpenBabel /
- Hands-on: Drawing and optimizing small Avogadro)
molecules

Module 6: Protein-Ligand Docking -


Theory
- Molecular docking principles
- Scoring functions, algorithms
- Rigid vs flexible docking
- Overview of AutoDock Vina Lecture +
Week 2: Day 1 10:00 AM – Hands-on
Docking and (10-8-2025) Module 7: Protein-Ligand Docking – 3:00 PM (AutoDock Vina /
Virtual Practical Tools)
Screening - Tautomers and ionization states
Week Day Session Title / Modules Time Activity Type

- Hands-on: Preparing ligands and receptor


with AutoDock Tools
- Hands-on: Docking using AutoDock Vina
- Analyzing results (binding poses, scores)

Module 8: Virtual Screening


- Hands-on: Running a virtual screening
campaign

Module 9: Protein-Protein Docking -


Theory
- Principles of protein-protein interactions
- Algorithms (FFT-based, shape
complementarity) Lecture +
Day 2 10:00 AM –
- Software overview: HADDOCK, ClusPro, Hands-on (Online
(12-8-2025) 2:00 PM
ZDOCK Server)
Module 10: Protein-Protein Docking -
Practical
- Hands-on: ClusPro docking
- Interface analysis

Module 11: Data Analysis & Visualization


- Basic statistics
Day 3 - Visualizing docking results 10:00 AM – Lecture + Hands-on
(14-8-2025) 2:00 PM (Online Server)
Module 12: Project Kick-off & Literature
Review
- Project phase introduction
Week Day Session Title / Modules Time Activity Type

- Group formation
- Guidance on literature search

Module 13: MD Simulation - Basics

- Principles of MD (force fields, ensembles)


- Periodic boundary conditions
- Software overview (GROMACS)
Day 1
Lecture +
(17-8-2025) 10:00 AM –
Module 14: MD Setup - Practical Hands-on
3:00 PM
(Colab / WSL)
- System prep: topology generation
- Solvation, ion addition
- Hands-on: GROMACS setup

Module 15: MD Simulation - Equilibration


& Production Run
Week 3: - NPT/NVT equilibration
Molecular - Production run (e.g., 10 ns)
Dynamics - Hands-on: Running simulations
Simulation Day 2
(21-8-2025) Module 16: MD Analysis - Basics
- Trajectory visualization (VMD) Lecture +
- RMSD, RMSF, Rg, hydrogen bond 10:00 AM – Hands-on
analysis 3:00 PM (MDAnalysis / plotly /
- Adv: Principal Component Analysis (PCA) gmxMMPBSA)
- Adv: Free energy calculations (MM/PBSA)
- Hands-on: MDAnalysis / plotly tools
- Hands-on: PCA on trajectory
Week Day Session Title / Modules Time Activity Type
Module 17: Project Work - Protein
Modeling & Virtual Screening
- Read literature, identify target protein Online Project Work
Day 1 - Model if necessary
- Prepare ligands, perform virtual screening
- Mentors available for guidance
Module 18: Project Work - Short MDS &
Analysis Project Work
Day 2 - Set up a 50 ns MD simulation
- Perform basic and advanced analysis Online
- Prepare results for presentation
Module 19: Project Presentations
Week 4: - Student presentations on methodology,
Project results, and conclusions
Presentation - Q&A session Online Presentation +
Day 3 Discussion
Module 20: Workshop Wrap-up
- Feedback session
- Certificate distribution

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