Cookiecutter template for a Python package.

PSICHIC (pronounced Psychic) - PhySIcoCHemICal graph neural network for learning protein-ligand interaction fingerprints from sequence data

Cookiecutter for Python packages based on MDAnalysis

Code accompanying our blog post on a stronger docking baseline for Alpha Fold 3 docking

Computational Chemistry/Biochemistry/Biophysics list of tools

Modelling protein conformational landscape with Alphafold

Cryptic pocket prediction using AlphaFold 2

A curated list of resources for using LLMs to develop more competitive grant applications.

Python Data and Scripting course for computational chemists

Evaluation of physicochemical and ADMET properties as an important stage of the drug design process – prediction, interpretation, and optimization

Deep generative models of 3D grids for structure-based drug discovery

A Machine Learned Molecular Mechanics Force Field with integration into GROMACS and OpenMM

Ligand Binding Site detection using Deep Learning

NMR Chemical Shifts from Molecular Dynamics Simulation

The Open Free Energy toolkit

a pipeline for running MD simulations in the presence of probe molecules for druggability assessment

MDANCE is a flexible n-ary clustering package for all applications.

A collections of scripts for working molecular dynamics simulations

Molecular Dynamics on Google Compute Engine, AWS (Amazon Web Services) and other Cloud Computing services

RG35XX Custom Firmware Documentation

The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems, compatible with the AMBER and OpenMM simulation packages.

Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention

NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

LOOS: a lightweight object-oriented structure analysis library