Getting Started with BioBB and PMX: Open-Source Tools for Biophysical and Medicinal Chemistry Simulations

This is a one-off Ambassador Program workshop jointly organised with and supported by the Latvian Institute of Organic Synthesis. The one day workshop is aimed at medicinal chemists and covers the theory and hands-on of protein MD setup using BioBB and protein-ligand relative binding free energy calculation using GROMACS/PMX.

Date: 24 April 2024
Venue: Latvian Institute of Organic Synthesis in Riga, Latvia


10:00 – 11:20 BioBB – Interoperable and reproducible biomolecular simulation workflows using BioExcel Building Blocks (BioBB)

11:20 – 11:40 Coffee break

11:40 – 13:00 BioBB hands-on tutorial: protein MD setup with Jupyter Notebooks and BioBB

13:00 – 14:00 Lunch break

14:00 – 15:20 Introduction to free energy calculations

15:20 – 15:40 Coffee break

15:40 – 17:00 PMX hands-on tutorial: protein-ligand relative binding free energy calculation