cloud-pkumdl/dsh-pdb

README excerpt

dsh-pdb Protein Design for Binder — an agent-driven workflow orchestration layer for protein binder design. Note: pdb here stands for P rotein D esign for B inder — not the Protein Data Bank. Why Most protein design tools (RFdiffusion, ProteinMPNN, AlphaFold2, ESMFold, Rosetta...) are powerful but command-line only, fragmented, and hard to chain . Running a full binder design campaign means manually stitching together a dozen scripts, tracking intermediate files by hand, and re-planning when a branch fails — with no unified view of what's been tried. dsh-pdb unifies these tools under a single agentic pipeline . An AI agent proposes a design plan; you review and refine it; the pipeline executes and reports back — with every step visualized as a living DAG. Core Idea Machine plans, human reviews, the graph is the alignment interface. Unlike cryoSPARC (human authors the workflow, machine executes, graph is a record), dsh-pdb inverts control: 1. Agent proposes — the agent generates an execution plan as a DAG (nodes = steps/strategies, edges = dependencies/derivations). 2. Human reviews — you see the plan as a flowchart, then approve, prune, or graft branches before anything runs. 3. Pi…

Category