Postdoc @cole-group developing MM force fields. Previously PhD student @michellab developing methods for alchemical free energy calculations (especially absolute binding free energy calculations).
Some of my scientific projects:
- Robust automated equilibration detection for molecular simulation
- Automated adaptive alchemical absolute binding free energy calculations
- Correcting molecular mechanics alchemical free energy calculations using machine learning potentials
- Comparing receptor-ligand restraint schemes for alchemical absolute binding free energy calculations (and publication)
Some of my (mainly) python code projects and contributions:
Contributed To
- BioSimSpace: An interoperable Python framework for biomolecular simulation
- BioSimSpace Tutorials: Contributed the ABFE tutorials
- Sire: A molecular modelling framework
Personal Projects
- A3FE: A package for running automated, adaptive, absolute binding free energy calculations
- RED: A package for robust equilibration detection for molecular simulation
- maize-biosimspace: BioSimSpace nodes for the maize workflow manager
Personal Miniprojects
- SQUID: An interactive display for
squeue - K2DG: Simple CLI tool for converting binding affinities and dissociation constants
- K2DG Streamlit App: Streamlit app for K2DG
