Program to find drug-like RNA-ligand binding pockets.

Scripts to run AlphaFold3, Boltz-1 and Chai-1 with MMseqs2 MSAs and custom templates.

Very flexible tools for plotting and analyzing all kinds of RNA structure data

Official implementation of All Atom Diffusion Transformers

Geometric Deep Learning @ University of Cambridge

PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.

Reversible molecular simulation

Automatic atomic model building program for cryo-EM maps

Send data to and from pymol from a remote server (e.g. a cluster running deep learning workflows)

AlphaFold 3 inference pipeline.

Official repository for the Boltz-1 biomolecular interaction model

Python pipeline to generate OpenKnotScores for Eterna sequence libraries

Metrics for assessing 3D molecular structures.

Simple Scalable Discrete Diffusion for text in PyTorch

CodonTransformer: The ultimate tool for codon optimization, optimizing DNA sequences for heterologous protein expression across 164 species.

Chai-1, SOTA model for biomolecular structure prediction

Joint embedding of protein sequence and structure with discrete and continuous compressions of protein folding model latent spaces. http://bit.ly/cheap-proteins

Pointcept: a codebase for point cloud perception research. Latest works: Sonata (CVPR'25), PTv3 (CVPR'24 Oral), PPT (CVPR'24), MSC (CVPR'23)

Flexible and scalable template based on PyTorch Lightning + Hydra. Efficient workflow and reproducibility for rapid ML experiments.

[ICLR 2024] "Latent 3D Graph Diffusion" by Yuning You, Ruida Zhou, Jiwoong Park, Haotian Xu, Chao Tian, Zhangyang Wang, Yang Shen

[ICLR 2024] The implementation for the paper "Space Group Constrained Crystal Generation"

This repository houses all the scripts and notebooks utilized for generating, analyzing, and validating the mdCATH dataset. Some user examples are also available.

Code for the tutorial/review paper for RL-based-fine-tuniing. In this code, we especially focus on the design of biological sequences like DNA (enhancers) and RNA (UTRs) design.

PINDER: The Protein INteraction Dataset and Evaluation Resource

Protein Ligand INteraction Dataset and Evaluation Resource

In-silico design pipeline for evaluating protein structure diffusion models.

[ICML'24] Adsorbate Placement via Conditional Denoising Diffusion

Evaluation dataset for AI systems intended to benchmark capabilities foundational to scientific research in biology