entity-small-molecule

AutoDock Vina

Differentiable, Hardware Accelerated, Molecular Dynamics

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

Molecular Processing Made Easy.

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).

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)

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

Molsystem provides a general class for handling molecular and periodic systems

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.

Python module for quantum chemistry

This repository contains code for the paper: Beyond Generative Models: Superfast Traversal, Optimization, Novelty, Exploration and Discovery (STONED) Algorithm for Molecules using SELFIES

A comprehensive macromolecular library

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.