protflow

What problem does it solve?

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.

Core Features & Use Cases

• Orchestrates multi-step design pipelines across RFdiffusion, LigandMPNN/ProteinMPNN/SolubleMPNN, ESMFold, ColabFold (AF2), AlphaFold3, Boltz, Caliby, Frame2Seq, ProteinGenerator, PLACER, AttnPacker, SigmaDock, Rosetta, GROMACS, DSSP, FPocket, Propka, TM-align, RMSD/biopython metrics behind a single Poses + JobStarter + Runner API.
• Supports SLURM array jobs and local execution, with per-pose tracking in a pandas-backed Poses object and a consistent on-disk layout for inputs, intermediate outputs, and scores.
• Tracks residue motifs across generative steps using ResidueSelection and remapping after diffusion, enabling motif persistence through design campaigns.
• Extends pipelines by subclassing Runner to add new tools, wiring tool paths and Python environments via a config system, and robust debugging wrappers for failure recovery.

Quick Start

Load input poses and run a sample multi-tool pipeline (RFdiffusion → LigandMPNN → ESMFold) with a unique prefix and a configured jobstarter.