bio-pharmacophore-modeling SKILL.md skillA
bio-pharmacophore-modeling from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-pharmacophore-modeling@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-chemoinformatics-pharmacophore-modeling/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 19,088 bytes
- Repository stars
- 662
- License
- MIT
Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al. 2023), Pharmer / Pharmit for search, and PharmacoForge for protein-pocket-conditioned pharmacophore generation (Flynn et al. 2025), covering ligand-based pharmacophores from active-set alignment and receptor-based pharmacophores from binding-pocket geometry. Explicitly handles feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use…
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
## Version Compatibility Reference examples tested with: RDKit 2024.09+, Pharmit web service, and PLIP 2.4+ (interaction analysis). Verify the deployed Pharmit/Pharmer interface and query format before automation. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show rdkit` then `help(rdkit.Chem.Pharm3D)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Pharmacophore Modeling Build 3D pharmacophore queries that capture the essential interaction features of a ligand-target binding event. A pharmacophore is the *spatial arrangement of pharmacophore features* (donor, acceptor, hydrophobe, aromatic, charged) sufficient for activity, abstracted from any specific chemotype. Use pharmacophores for scaffold hopping, virtual-screening prefilters, and cross-target SAR transfer. Derive interaction features directly from a co-crystal when available, use apo2ph4 to derive models from an apo pocket (Heider et al. 2023), or align known actives for a ligand-based model. PharmacoForge generates candidate 3D… …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-pharmacophore-modeling@sha256:a060fbd45483a963The line at the top of this page pins the label git:20260821.2d1b678, 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_isb6gkvaqytpqood)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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- 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
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_isb6gkvaqytpqood GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-pharmacophore-modeling GET https://markdownregistry.com/api/v1/blob/a060fbd45483a96353d9c61afcf627d974b0370fcc8f501ddbb9f4efdc6c70b7
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.