Menu

Individual skill

proteinmpnn

0upvotes

Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. 2022, github.com/dauparas/ProteinMPNN). Reach for this skill to run sequence design on RFdiffusion backbones, to redesign one chain of a PDB while holding interface residues fixed, or to generate a temperature-swept set of sequences for downstream folding.

resources/skills/proteinmpnn/SKILL.md

Read pinned source

Source commit 357d1a980056e191f380d0e01ec4fbc7cf529d1b

What was checked

Matches the observed repository HEAD
Yes
Scanner rules are current
No
Repository scan complete
No
Skill scan complete
No
Observed behavior
Not checked yet
Last checked
Nov 3, 2026

These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.

Install this skill

Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.

An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.

Repository context

Repository stars (not skill ratings)
5,495
Repository last updated
Nov 8, 2026
License
Apache-2.0

Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.

Files and excerpt

File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.

Browse files
Read excerpt

# ProteinMPNN

ProteinMPNN is the default inverse-folding step in the binder pipeline: a
message-passing network that sees backbone geometry only, so it is the right
choice when the design surface is protein–protein and the wrong one as soon as
a ligand, nucleic acid, or metal is part of the interface — `ligandmpnn` adds
those atoms to the graph with a near-identical CLI, and `solublempnn` swaps in
weights trained on soluble structures for an expression-biased prior. Code and
weights are MIT (github.com/dauparas/ProteinMPNN). The model is small enough
to run on CPU — for a handful of sequences on one backbone that is seconds and
usually faster than dispatching a remote job; a GPU helps for batched
campaigns (hundreds of backbones or large `--num_seq_per_target`). Either way
the repo is cloned in-job — there is no PyPI dist and the checkpoints are
bundled in the repo.