Focus on:  Hide Contributions
Africa/Johannesburg English Login

Accelerated free energy calculations using open-source tools

→ Africa/Johannesburg
Description

In this workshop, you will learn how to use free energy tools with an application to drug discovery. We will use open-source free energy tools and the Galaxy Platform (BRIDGE) to calculate absolute and relative free energies of protein-ligand binding with T4 Lysozyme as a usecase. Setting up free energy molecular simulations, using scripts, the Linux command line and using HPC resources can be complex. Further not all steps are repeatable. With the Galaxy Project platform, BRIDGE and Galaxy Comp Chem we aim to provide a web application to assist researchers in conducting repeatable computer simulations and analysis using curated workflows.

Target Audience: Are you keen to learn how to calculate absolute and relative free energies of protein-ligand binding for drug discovery? 

Prerequisites: At least an undergraduate level chemistry, biology, physics or similar background. Some experience viewing and working with molecular structures. Have a read through the Galaxy training material on GitHub - https://galaxyproject.github.io/training-material/topics/computational-chemistry/ 

Special requirements: Bring a laptop. All remote computing resources will be provided. Install molecular viewer e.g. VMD. If possible have Virtualbox with Ubuntu/Centos installed.

README - Free Energy BRIDGE workshop
Registration
Participants
2 / 30
Apply for participation
Contact
    • 08:00 → 09:00
      Registration 1h
    • 09:00 → 10:30
      Intro to Galaxy 1h 30m

      Presentation: What is Galaxy Project, BRIDGE and Galaxy Comp Chem? What tools and compute are available nationally and internationally?
      Interactive Session: Intro to Galaxy

    • 10:30 → 11:00
      Morning break 30m
    • 11:00 → 12:30
      Presentation: What is free energy? 1h 30m

      Presentation: What is free energy? Application to drug discovery and protein-ligand binding. Why not docking? Overview of the landscape tools/methods.
      Interactive session:
      Absolute binding
      Relative binding

    • 12:30 → 13:30
      Lunch 1h
    • 13:30 → 15:00
      Presentation: Tools for analysis and convergence. Interactive session: Analysis 1h 30m
    • 15:00 → 15:30
      Afternoon break 30m
    • 15:30 → 17:00
      Interactive session: Analysis Open session: Bring your own proteins and molecules. (fill in the survey here - https://forms.gle/r9LdRc76EpG7aaHA9)
    • 17:00 → 17:05
      End of Workshop 5m
Powered by Indico