One Month International Bioinformatics Workshop - Advanced MD Simulation and DFT 3rd Edition - 2026

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DECODE LIFE WORKSHOP

Workshop Highlights

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Upskilling

Workshop will help in learning core Bioinformatics skills for cutting edge research.

Workshop Material

Workshop material along with video recording of each session.

Networking

Instructor and participants will be from different corners of the world where participants will be encouraged for collaborations.

Global Instructors

Instructors from diverse global institutions.

GLOBAL EXPERTS MEET UP

Course Trainers

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Dr. Avinash Mishra

CEO at Growdea Technologies Pvt Ltd.Indo-Australian Gold fellow at Griffith University, Australia.
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Suphal Sen

Vellore Institute of Technology, Vellore
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Dr. Shivangi Agarwal

Former Post Doctoral Associate at University of Illinois, Chicago, USA.
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Akshat Jha

Machine learning engineer at Growdea Technologies Pvt Ltd.

OUR EXPERIENCE

Who we are

 Decode life is a group of enthusiastic researchers, who are aimed to (de)code the life sciences. Our goal is to create a self sustained system through cross learning and joining hands together to address the problems that matter the most. With the availability of large data, Bioinformatics has become an integral part for almost every biomedical lab. We wanted to fill in the niche and train the next generation of data scientists..

ONE MONTH COMPREHENSIVE BIOINFORMATICS TRAINING

Schedule of the workshop

UPSKILL YOUR PORTFOLIO WITH GLOBAL EXPERTS

From

05 Aug, 2026

To

30 Aug, 2026

7:30 - 8:30 PM IST
05 Aug- 30 Aug, 2026
Schedule of Workshop
DayDateTopic
Wednesday05-Aug-2026Introduction to MD Simulation Analysis
– Overview of MD Simulations
– Importance of Post MD Simulation Analysis
– Common software tools and packages for analysis
Thursday06-Aug-2026Data Preparation and Cleaning
– Data file formats (e.g., XTC)
– Data preprocessing and cleaning
– Handling missing or corrupted data
Friday07-Aug-2026Trajectory Analysis
– Extracting information from MD trajectories
– Calculating structural parameters (RMSD, RMSF)
– H-Bond Calculation
– Center of Mass Distance
Saturday08-Aug-2026OFF
Sunday09-Aug-2026OFF
Monday10-Aug-2026Free Energy Calculations
– Overview of free energy methods (e.g., MM/PBSA, MM/GBSA)
– Performing binding free energy calculations
Tuesday11-Aug-2026Principal Component Analysis (PCA)
– Understanding PCA and its applications in MD analysis
– Plotting PCA
Wednesday12-Aug-2026Umbrella Sampling MD Simulation
– Theoretical Basis of Umbrella Sampling
– Preparing for Umbrella Sampling
– Running Umbrella Sampling Simulations
– Analyzing Umbrella Sampling Data
Thursday13-Aug-2026Introduction to Coarse-Grained MD
– Basics of coarse-graining: key concepts and benefits
– Overview of popular force fields
– Applications of coarse-grained MD in biomolecular simulations
Friday14-Aug-2026System Preparation for Coarse-Grained MD
– Steps to map an all-atom system to a coarse-grained representation
– Preparing input files
Saturday15-Aug-2026OFF
Sunday16-Aug-2026OFF
Monday17-Aug-2026Running Coarse-Grained MD Simulations
– Workflow: energy minimization, equilibration, and production runs
– Key considerations for coarse-grained simulations
Tuesday18-Aug-2026Analysis of Coarse-Grained Simulations & Applications
– Extracting key metrics: area per lipid, bilayer thickness, self-assembly
– Tools and methods for coarse-grained simulation analysis
– Modeling protein-lipid and protein-protein interactions
– Applications in large biomolecular complexes and self-assembly studies
Wednesday19-Aug-2026Introduction to Steered MD
– Principles of Steered MD: applying external forces in simulations
– Key applications: protein-ligand interactions, unfolding studies
Thursday20-Aug-2026Setting Up & Analysis of Steered MD Simulations
– Configuring Steered MD simulations: reaction coordinates and force constants
– Defining pulling paths and setting up input files
– Analyzing force-distance profiles and calculating work done
– Linking Steered MD results to physical properties (e.g., binding affinity)
Friday21-Aug-2026Advanced Techniques in Steered MD
– Multi-directional pulling and dynamic force spectroscopy
– Optimizing pulling velocities and force constants
Saturday22-Aug-2026off
Sunday23-Aug-2026off
Monday24-Aug-2026A brief intro to quantum chemistry & DFT
– Classical vs. quantum methods
– Electronic concept
– Introduction to DFT
Tuesday25-Aug-2026DFT theory and practical aspect
– Functionals
– Basis sets
– SCF
– Entry to Computational Platform ORCA 6.1
Wednesday26-Aug-2026Platform preparation
– Graphical tools (ChemCraft and Avogadro)
– Input file preparations
– Understanding the coordinate concept
– Live task
Thursday27-Aug-2026Calculations & Analysis
– Running ORCA
– Geometry optimization and Frequency analysis
– Understanding the keywords
– Energy calculation
– Charge distribution
Friday28-Aug-2026Calculations & Analysis
– HOMO-LUMO identification
– Molecular Orbitals
– Single-point refinement
Saturday29-Aug-2026Calculations & Analysis
– Complex optimization
– Binding energy-Free energy
– Solvation model
– Thermochemistry
– TD-DFT study
Sunday30-Aug-2026Calculations & Analysis
– Intro to GOAT Algorithm – automated reaction tool
– Metal complex simulation
– Use of ZORA
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International Participants

$ 30

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