entity-small-molecule

Differentiable, Hardware Accelerated, Molecular Dynamics

AutoDock Vina

End-To-End Molecular Dynamics (MD) Engine using PyTorch

Some useful RDKit functions

Codes for our paper "Programming Biomolecular Interactions with All-Atom Generative Model"

Reaction fingerprints, atlases and classification. Code complementing our Nature Machine Intelligence publication on "Mapping the space of chemical reactions using attention-based neural networks" (http://rdcu.be/cenmd).

Molecular Processing Made Easy.

Source code for molecular graphics program UCSF ChimeraX

Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping

A Pharmacophore MultiToolkit designed to simplify and streamline the detection, generation, analysis, comparison, and application of pharmacophore models in drug-design strategies.

Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

Molsystem provides a general class for handling molecular and periodic systems

Official Github for "PharmacoNet: deep learning-guided pharmacophore modeling for ultra-large-scale virtual screening" (Chemical Science)

A comprehensive macromolecular library

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

Prediction of binding residues for metal ions, nucleic acids, and small molecules.

IF-SitePred is a method for predicting ligand-binding sites on protein structures. It first generates an embedding for each residue of the protein using the ESM-IF1 (inverse folding) model, then performs point cloud clustering to identify binding site centers.

NequIP is a code for building E(3)-equivariant interatomic potentials

A package to identify matched molecular pairs and use them to predict property changes.