Method development

Methods I develop

I write the methods behind my simulations: QM workflows with machine-learned potentials and transition-state searches, QM/MM charges derived inside the protein, and MM set-up and analysis. Each is open source on GitHub.

QM → MM

protonation-optimizer

★ 20

Picks histidine tautomers (HID/HIE/HIP) from PropKa3 pKa values plus xTB energies of each local environment, before MD.

Python · xTB · PropKa3 · MDTraj · blog post

QM/MM

QMMESP

★ 8

RESP charges for ligands computed inside the protein with electrostatically embedded QM/MM, written straight into Amber prepi files.

Python · PySCF / ORCA · Multiwfn · blog post

QM

MLatom-ORCA-interface

Couples the AIQM2 potential in MLatom with ORCA's optimiser and relaxed scans, for cluster-model calculations.

MLatom · ORCA · AIQM2 · blog post

QM

gxtb-pymol-interface

A PyMOL plugin that runs xTB and g-xTB: optimisations, frequencies, NEB paths and IRC-like relaxations from the viewer.

PyMOL · Qt · xTB / g-xTB

MM

MDTunnel

Moves a ligand along a protein tunnel one sphere at a time, minimising at each step, and returns an energy profile.

OpenMM · OpenFF · AutoDock Vina

Also on GitHub

2026
mdprepPython
★ 2
2026
EVBPython
2025
ala2_metaD_GirsanovData and scripts for my initial test using girsanov reweighting Python
2025
LB-Caverdock_cloneTry at making my own CaverDock LB calculations using Vina for further testsPython
2022
ABPy_contributionsRunning dockings from the notebook enviromentJupyter Notebook
2018
2018
BandProfilerPython program to calculate the intensity of multiple parts of a SDS-PAGE gel, acrilamide gel,inmunodetection membranes, etcPython
2017
compbiolab_v0.1.4compbiolab Python module v0.1.5Python
2017
compbiolabcompbiolab Python modulePython