entity-small-molecule

Differentiable, Hardware Accelerated, Molecular Dynamics

AutoDock Vina

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

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

Some useful RDKit functions

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.

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

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

Source code for molecular graphics program UCSF ChimeraX

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

Molsystem provides a general class for handling molecular and periodic systems

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

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

a molecular descriptor calculator

An automated framework for generating optimized partial charges for molecules

📐 Symmetry-corrected RMSD in Python

Force fields produced by the Open Force Field Initiative