Protein Design

Generative models and language models for protein sequence and structure design.

Tools Awesome Lists Getting Started

Tools

Generative Design

ProteinMPNN Message passing for inverse folding RFDiffusion Diffusion model for backbone generation ColabDesign Notebooks for AfDesign, TrDesign, ProteinMPNN ESM-IF1 Inverse folding with ESM EvoDiff Discrete diffusion for sequences ProtGPT2 GPT-2 based sequence generation BindCraft Binder design LM-Design / ByProt Language model design ProteinSolver Graph neural network for constraint-based design ECNet Fine-tunable fitness/function prediction

Protein Language Models

ESM-2 Protein embeddings (8M–15B params) ProtTrans Transformer embeddings for proteins AMPLIFY ESM2 reimplementation with open training PoET Variant effect prediction and generation EvoProtGrad MCMC-based directed evolution

Communities

OpenBioML

Decentralized collaborative research community for open source ML and open science to accelerate biotechnology.

Focus: Biotechnology, drug discovery, protein engineering
Platform: Discord

Key Research Groups

Baker Lab (UW) — Protein design
Coley Group (MIT) — Synthesis planning, ML for chemistry

Awesome Lists

Protein design papers Protein design tools AI protein design

Getting Started


conda create -n protdesign python=3.10
conda activate protdesign
 
pip install fair-esm biopython

Targets, Response & Repurposing Protein Structure