Learning Binding Affinities via Fine-tuning of Protein and Ligand Language Models

Endstate corrections from MM to QML potential

Deep Potential driven molecular dihedral scan toolkit

Support for OpenMM units as pydantic fields

Molecular Library Toolbox

A Unified Approach to Protein Engineering

Data generation and submission scripts for the QCArchive ecosystem.

moldrug (AKA mouse) is a Python package for drug-oriented optimization on the chemical space ​

Python-based GUI to collect Feedback of Chemist in Molecules

Language models for drug discovery using torchrl

CReM: chemically reasonable mutations framework

Practical Cheminformatics Tutorials

A package for all physics based/related models

A foundational package for molecular predictive modelling

A reactive notebook for Python — run reproducible experiments, query with SQL, execute as a script, deploy as an app, and version with git. All in a modern, AI-native editor.

Code and Pre-Trained Models for "AttnPacker: An end-to-end deep learning method for protein side-chain packing"

A web app to convert a PyMOL PSE file or PDB file to a easy to implement NGL.js view that can be implemented easily on any site

Pose butcher segments a ligand into categories

Torch-based internal coordinate geometry optimization

Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits

Algorithms for various Network Layouts and Tooling for planning FE Calculations

Uni-Dock: a GPU-accelerated molecular docking program

To enumerate combinations of R-groups for a molecule pair and prune down to logical options for FEP intermediates.

A robust template for new python projects

MACE-OFF23 models