OVO, an open-source ecosystem for de novo protein design
OVO (pronounced "oh-voh") consolidates models, workflows, data management, and interactive visualization into a scalable, high-performance, infrastructure-agnostic platform for de novo protein design. OVO features Nextflow-based workflow orchestration, a storage layer, and both command-line and web interfaces that democratize scaffold design, binder design and diversification, and validation workflows.
Ovo, an Open-Source Ecosystem for De Novo Protein Design, David Prihoda, Marco Ancona, Tereza Calounova, Adam Kral, Lukas Polak, Hugo Hrban, Nicholas J. Dickens, Danny Asher Bitton bioRxiv 2025.11.27.691041; doi: https://doi.org/10.1101/2025.11.27.691041
🐣 Getting started
To get started with OVO, please refer to the User Guide.
To preview the OVO web app (without the ability to submit jobs), see the OVO Demo Server.
▶️ Demo video
https://github.com/user-attachments/assets/7b339fa6-c6de-467d-90d0-5cd15f83c498
🧬 Methods & Acknowledgments
We gratefully acknowledge the authors and developers of the following methods and tools available from OVO:
| Method Name | Description | Reference / Paper | Link |
|---|---|---|---|
| RFdiffusion | Diffusion-based protein structure generation | Watson et al. 2023 | GitHub |
| ProteinMPNN | Protein sequence design for fixed backbones | Dauparas et al. 2022 | GitHub |
| LigandMPNN | Atomic context-conditioned protein sequence design | Dauparas et al. 2025 | GitHub |
| PyRosetta FastRelax | Binder sequence design protocol | Bennett et al. 2023 | GitHub |
| AlphaFold2 / ColabDesign | Deep learning-based protein structure prediction | Jumper et al. 2021 | GitHub (AlphaFold2), GitHub (ColabDesign) |
| BindCraft | Binder design using AF2 backpropagation | Pacesa et al. 2024 | GitHub |
| Boltz | Deep learning-based protein structure prediction | Wohlwend et al. 2024, Passaro et al. 2025 | GitHub |
| ESM-1v | Protein language model for variant effect | Meier et al. 2021 | GitHub |
| ESM-IF | Inverse folding with protein language models | Hsu et al. 2022 | GitHub |
| DSSP | Secondary structure assignment | Kabsch & Sander 1983, Joosten et al. 2010 | GitHub |
| PEP-Patch | Protein surface patches analysis | Kufareva et al. 2023 | GitHub |
| Protein-Sol | Protein solubility prediction | Hebditch et al. 2017 | Web |
🛠️ Development
OVO is an open-source project and we welcome contributions from the community.
Please refer to the Developer Guide for information on how to contribute to OVO.
1 maintainer
Release files for ovo 1.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| ovo-1.1.0.tar.gz | 3.0 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| ovo-1.1.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 6.1 MB
Release files / ovo-1.1.0.tar.gz
| Download URL | ovo-1.1.0.tar.gz |
|---|---|
| Size | 3.0 MB |
| Tags | Source |
|
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twine/4.0.2 CPython/3.8.15
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Release files / ovo-1.1.0-py3-none-any.whl
| Download URL | ovo-1.1.0-py3-none-any.whl |
|---|---|
| Size | 3.2 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/4.0.2 CPython/3.8.15
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