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

📐 Symmetry-corrected RMSD in Python

A Euclidean diffusion model for structure-based drug design.

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

Parameter/topology editor and molecular simulator

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

3D ligand-based pharmacophore modeling

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

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)

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

Calculation of interatomic interactions in molecular structures

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.

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

🚂 Python API for Emma's Markov Model Algorithms 🚂

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

Molecular Processing Made Easy.