Codebase for Germinal, a broadly enabling generative pipeline for efficient generation of epitope-targeted de novo antibodies.

A benchmark dataset for protein-ligand co-folding prediction

"DeepCode: Open Agentic Coding (Paper2Code & Text2Web & Text2Backend)"

An open-source platform for developing protein models beyond AlphaFold.

DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models

User friendly and accurate binder design pipeline

Chai-1, SOTA model for biomolecular structure prediction

PINDER: The Protein INteraction Dataset and Evaluation Resource

A subset of PyTorch's neural network modules, written in Python using OpenAI's Triton.

Public RFDiffusionAA repo

Protein Graph Library

A geometry-complete diffusion generative model (GCDM) for 3D molecule generation and optimization. (Nature CommsChem)

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

A geometry-complete SE(3)-equivariant perceptron network (GCPNet) for 3D graphs. (Bioinformatics)

Generation of protein sequences and evolutionary alignments via discrete diffusion models

Code for "A Deep Learning Framework for Flexible Docking and Design"

Structure-conditioned masked language modeling for protein sequence design

✌🏻 Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures (NeurIPS 2022)

This is the official code release for Bayesian Flow Networks.

A list of manuscripts/tools using diffusion on biological enttieis

Antibody-Antigen Docking and Affinity Benchmark

Diffusion-based all-atom protein generative model.

Code for the ProteinMPNN paper

A playbook for systematically maximizing the performance of deep learning models.

Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation

Predict the structure of immune receptor proteins