In this post, I’ll link to a few training materials and software packages that might be useful to new starters in our lab (or elsewhere). I intend for this to be updated regularly, so please feel free to suggest changes or additions. A big thank you to everyone that has put these online resources together, we find them invaluable!

Workshops

CCP-BioSim. Excellent set of training modules and Youtube channel. Subjects include biomolecular dynamics, FESetup, BioSimSpace and Python for biomolecular modelling.

Bespoke-fit. A workshop describing the use of Open Force Field’s bespoke-fit package for fitting molecule-specific torsion parameters, given by own Josh Horton.

TeachOpenCADD. Really useful set of talktorials on the use of open source cheminformatics tools for computer-aided drug design.

[Data science.][turing]

Research Software

[QUBEKit.][qubekit]

Open Force Field. We’re very happy to be working with the OpenForceField initiative, and we make extensive use of their software infrastructure in our work. A good place to start is with the documentation examples on building and interacting with molecules, and a set of notebooks, which show how to use the toolkit to parameterise a system and run a short simulation in OpenMM.

[OpenMM.][openmm]

BioSimSpace / SOMD. Python framework for biomolecular simulation, includes a set of tutorials for common simulation types. Our own tutorials written with Julien Michel’s lab show how to use SOMD in protein-ligand binding and hydration free energy calculations with different force fields.

[RDKit.][rdkit]

[DeLinker.][delinker]

[Gnina.][gnina]

[ONETEP.][onetep]

Miscellaneous

[Pymol.]

[Machine learning.]