Protein design workflows series kick off with Protflow and Ovo

On January 20, the protein design community kicked off a new Protein Design Workflows meeting series focused on how people are building, running, and scaling protein design pipelines in practice.

The goal of this series is simple: create a space where developers and users can present real workflows, compare approaches, and identify opportunities for shared infrastructure and collaboration. As protein design tools continue to proliferate, stitching them together into reliable, reusable pipelines has become a major challenge—and a major time sink.

The first meeting featured two workflow libraries that approach this problem from complementary angles.

Automating pipelines with ProtFlow

Markus Braun (Graz University of Technology) presented ProtFlow, an open-source Python workflow library designed to reduce the overhead of pipeline development. ProtFlow focuses on modularity and consistency: individual design tools are wrapped as “Runner” objects, proteins are represented in a unified data structure that tracks metadata and scores, and job execution is abstracted so workflows can run across different compute environments. The emphasis is on letting designers spend more time optimizing protocols and less time managing files and formats.

An integrated ecosystem with Ovo

David Prihoda (MSD Czech Republic) introduced Ovo, an open-source ecosystem for de novo protein design that integrates workflow orchestration, data management, and visualization. Built around scalable workflow execution, Ovo aims to lower the barrier to running end-to-end design pipelines while supporting large-scale analysis and benchmarking. A key feature is its ProteinQC module, which computes sequence and structure descriptors to help contextualize designs against reference sets.

With strong attendance and an engaged discussion, this first session confirmed the appetite for shared conversations around workflow design. Future meetings will continue to feature community-developed pipelines and explore how collaboration could reduce duplicated effort across labs.

If you’re interested in presenting a workflow, suggesting tools to highlight, or joining the discussion, you can sign up HERE for suggesting a workflow to be presented or sign up to give a presentation HERE. 

For further discussion, join the Slack channel #protein-design-workflows or join the mailing list at  https://groups.google.com/g/protein-design-workflows. Contact Hope Woods if you have trouble joining. Also check out our Youtube playlist for uploaded talks on this. 

The next meeting will happen on February 3rd at 5pm CET / 4pm WET / 11am ET / 8am PT. Please check out the Rosetta Events calendar for details.