From 29 February - 10 days International Bioinformatics Workshop on - Molecular Dynamics Simulation Analysis (Advanced) by Decode Life.

From 29 February - 10 days International Bioinformatics Workshop on - Molecular Dynamics Simulation Analysis (Advanced)  by Decode Life.

Registration is open for 10 days Bioinformatics Workshop by DE<code>LIFE

Duration:  29 february - 10 March,  2024 ( Timing 6 PM Indian Standard Time)

✍️ Registration Link - https://decodelife.co.in/advancecourses/

Fees: Rupees 1200 for Indian Participants /USD 25 for International    Participants

Schedule

Date

Instructor

Topics

29 Feb,2024

Avinash

Introduction to MD Simulation Analysis

Overview of Molecular Dynamics (MD) Simulations

Importance of Post MD Simulation Analysis

Common software tools and packages for analysis

1 Mar,2024

Avinash

Data Preparation and Cleaning

Data file formats (e.g., XTC)

Data preprocessing and cleaning

Handling missing or corrupted data

2 Mar,2024


OFF

3 Mar,2024

Avinash

Trajectory Analysis

Extracting information from MD trajectories

Calculating structural parameters (RMSD, RMSF)

H-Bond Calculation

Center of Mass Distance

4 Mar,2024

Avinash

Free Energy Calculations

Overview of free energy methods (e.g., MM/PBSA, MM/GBSA)

Performing binding free energy calculations, Principal Component Analysis (PCA)

Understanding PCA and its applications in MD analysis

Plotting PCA

5 Mar,2024


OFF

6 Mar,2024

Suyash

Free Energy Landscape (FEL)

Understanding FEL and its applications in MD analysis

Plotting FEL

7 Mar,2024

Suyash

Introduction to Umbrella Sampling

Theoretical Basis of Umbrella Sampling

Collective Variables (CVs) and Bias Potentials

Advantages and Limitations

8 Mar,2024


OFF

9 Mar,2024

Suyash

Preparing for Umbrella Sampling

Defining the Reaction Coordinate

Selection of CVs

Generating Initial Structures

Choosing Umbrella Potentials

10 Mar,2024

Suyash

Running Umbrella Sampling Simulations, Analyzing Umbrella Sampling Data


Free Energy Profiles and Histograms


Wham (Weighted Histogram Analysis Method)


PMF (Potential of Mean Force) Calculation

Key Features :

E- Certificate of Participation.

Video recording and workshop material

Global expert course faculty from diverse Institutions.

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