OVO, an open-source ecosystem for de novo protein design

Official repository for the ProteinDJ protein design pipeline

A Nextflow pipeline for protein binder design

De novo therapeutic peptide design pipeline using RFdiffusion and ESMFold to hallucinate NaV1.7 pain-channel blockers locally on CPU

A modular, extensible peptide design pipeline with target preparation, backbone generation, sequence design, scoring, and ranking. Full local CPU pipeline, and backend hooks for RFpeptides, ProteinMPNN/LigandMPNN, and ColabFold.

De novo design of a miniprotein binder targeting the SARS-CoV-2 spike RBD using RFdiffusion, ProteinMPNN, and Rosetta. A step-by-step project integrating generative AI and structural bioinformatics.

Protein binder design GUI

RNA-seq counts to ranked de novo protein binder candidates, with full provenance back to the patient cohort.

Molecular dynamic simulation of RFdiffusion/ProteinMPNN designed HMERF mutated titin Ig152/Fn3-119 domain protein binder

Manage protein design processes

Design proteins in your terminal. A TUI agent for de novo protein design — free by default.

Protein convex binder design GUI

Open-source production control plane for protein-design pipelines (RFdiffusion → ProteinMPNN → Boltz/AlphaFold2). Start here: architecture, docs, dev tooling.

🧬 Lectures for course ML-protein-design

구조 기반 de novo 항체 설계

UC Berkeley MSSE Capstone Project: Evaluating & refining filtering strategies for de novo protein binders

De novo protein binder design pipeline: motif-scaffolded RFdiffusion + ProteinMPNN + AlphaFold2 self-consistency validation. PD-L1 reference example.

Python gRPC sidecar wrapping RFdiffusion (de novo protein backbone generation) for FoldForge.

Personalized lymphoma therapy design with Gemma 4, AlphaFold, RFdiffusion. Kaggle Gemma 4 Good Hackathon submission.

Iterative AlphaFold-Guided Nanobody Design for Lateral Flow Immunoassays