ligandmpnn SKILL.md skillA
ligandmpnn from pengqianhan/ai-human-research-os is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pengqianhan/ai-human-research-os/ligandmpnn@git:20260715.38d79bePins git:20260715.38d79be in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pengqianhan/ai-human-research-os
- Path
research-skills-hub/claude-science-skills/skills/ligandmpnn/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260715.38d79be, committed Jul 15, 2026
- Size
- 6,217 bytes
- Repository stars
- 3
- License
- MIT
Inverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al. 2023, github.com/dauparas/LigandMPNN). Reach for this skill to redesign the residues lining a binding pocket around a bound small molecule or cofactor, to design metal-coordinating sites where the geometry must be respected, or to get threaded designed-sequence PDBs out of any MPNN run.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# LigandMPNN LigandMPNN extends the ProteinMPNN graph with non-protein atoms — small molecules, nucleic acids, and metals are visible to the network — so it is the right inverse-folding tool whenever the design surface includes a bound ligand or cofactor that vanilla `proteinmpnn` would ignore. The same `run.py` is also the most convenient runner for the other MPNN families because, unlike the original ProteinMPNN script, it threads designs back onto the input structure and writes PDBs alongside the FASTA. Code and weights are MIT (github.com/dauparas/LigandMPNN). The model is small enough to run on CPU — for a handful of designs on one structure that is seconds and usually faster than dispatching, so the normal path is local with `pip install torch numpy biopython ProDy ml_collections dm-tree`; a GPU helps for batched campaigns. ## Running it ```bash pip install torch numpy biopython ProDy ml_collections dm-tree git clone --depth 1 https://github.com/dauparas/LigandMPNN.git ligandmpnn cd ligandmpnn sed -i 's/np\.int\b/np.int64/g' openfold/np/residue_constants.py # repo pins numpy 1.23; alias removed in >=1.24 bash get_model_params.sh ./model_params python run.py \ …
Read the whole file at its exact version.
How to install
mdr add pengqianhan/ai-human-research-os/ligandmpnn@sha256:004f25fe7caab394The line at the top of this page pins the label git:20260715.38d79be, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_3wjvcqclc2jy5bad)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Jul 15, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (6217 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
pengqianhan/ai-human-research-os · 3 stars · license MIT · pushed 2026-10-19 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_3wjvcqclc2jy5bad GET https://markdownregistry.com/api/v1/resolve?ref=pengqianhan/ai-human-research-os/ligandmpnn GET https://markdownregistry.com/api/v1/blob/004f25fe7caab394424fb7e2660b9428ad7079d0b9ff1d573079ab6340938396
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
More from pengqianhan/ai-human-research-os
Every file in pengqianhan/ai-human-research-os