Orchestrate protein-design pipelines across multiple tools via a unified API.
npx skills add https://github.com/LiorZ/protein-design-skills --skill protflow
Please help me install this Agent Skill. Skill: protflow Source: https://github.com/LiorZ/protein-design-skills/tree/main/skills/protflow Command: npx skills add https://github.com/LiorZ/protein-design-skills --skill protflow
ProtFlow provides a unified orchestration layer to build and run end-to-end protein-design campaigns by coordinating multiple design tools behind a single API, tracking results, and enabling reproducible workflows.
Load input poses and run a sample multi-tool pipeline (RFdiffusion → LigandMPNN → ESMFold) with a unique prefix and a configured jobstarter.
High-intent search queries and answers about installing and using this skill.
You orchestrate a multi-tool protein design pipeline by unifying multiple design tools behind a single API. This skill coordinates tools like RFdiffusion, LigandMPNN, and ESMFold while tracking results in a pandas-backed Poses dataframe for reproducible workflows.
Yes, you can run protein design workflows on a SLURM cluster. The orchestration layer supports SLURM-based array jobs alongside local execution to scale protein-design campaigns across high-performance computing environments.
To track residue motifs across diffusion steps in protein design, the pipeline uses ResidueSelection and remapping after diffusion. This enforces motif persistence through the various generative steps of a design campaign.
The best way to add new bioinformatics tools to an existing pipeline is by subclassing the Runner class. This extension method allows you to wire tool paths and Python environments via a config-driven path resolution system.
Yes, this pipeline orchestration supports AlphaFold3 and Boltz. It unifies these structure prediction tools with other design utilities behind a single Poses, JobStarter, and Runner API for standardized score merging.
To recover from failures during a protein design campaign, the orchestration layer provides robust debugging wrappers. These wrappers help manage standardized score merging and handle errors encountered during multi-step tool execution.
QuantumBFSSubmit, monitor, and diagnose Slurm cluster array jobs with pre-submit feasibility checks.
awslabsStandardize protein structure analysis workflows with PDB/mmCIF parsing, RMSD superposition, and binding pocket detection.
mims-harvardDesign protein therapeutics with RFdiffusion, ProteinMPNN, and ESMFold validation.
fuzzy-dynamicsAccess 20+ bioinformatics databases and analysis tools via CLI and Python.
