entity-small-molecule

AutoDock Vina

Differentiable, Hardware Accelerated, Molecular Dynamics

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.

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)

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.

Adds or removes hydrogen atoms to achieve the appropriate molecular protonation state for a user-specified pH range

WebGL accelerated JavaScript molecular graphics library

OpenMM is a toolkit for molecular simulation using high performance GPU code.

Python3 translation of AutoDockTools

Open-source foundation of the user-sponsored PyMOL molecular visualization system.

Interface for AutoDock, molecule parameterization