method-deep-learning

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

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

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

Differentiable, Hardware Accelerated, Molecular Dynamics

Toward High-Accuracy Open-Source Biomolecular Structure Prediction.

Code for running RFdiffusion

MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.

Comprehensive library for fast, GPU accelerated molecular gridding for deep learning workflows

A Euclidean diffusion model for structure-based drug design.

[NeurIPS2025 Spotlight 🔥 ] Official implementation of "UniSite: The First Cross-Structure Dataset and Learning Framework for End-to-End Ligand Binding Site Detection"

Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196

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

This package contains deep learning models and related scripts for RoseTTAFold

Training and inference code for ShEPhERD: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design [ICLR 2025 oral]

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.

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).

Predicting protein-ligand binding sites using deep convolutional neural network

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