bio-virtual-screening SKILL.md skillA
bio-virtual-screening 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-virtual-screening@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-virtual-screening/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 24,500 bytes
- Repository stars
- 662
- License
- MIT
Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking…
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: AutoDock Vina 1.2.5+, SMINA 2020-12+, GNINA 1.1+ for `rescore` (GNINA 1.3+ for the six-mode interface documented below), RDKit 2024.09+, meeko 0.5+, P2Rank 2.4+, ProDy 2.4+, pdb2pqr 3.6+. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `vina --version`; `gnina --version`; `smina --version` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Virtual Screening Screen chemical libraries against protein targets via molecular docking. Vina is the de-facto default, SMINA adds flexibility (Vinardo scoring, custom scoring), and GNINA adds CNN-based pose scoring (Top-1 redock 58%->73% over Vina, cross-dock 27%->37%). Deep-learning docking (DiffDock-L, EquiBind, NeuralPLexer) competes in pose accuracy, but physical validity is method- and dataset-dependent; the workflow therefore combines ML pose sampling with classical scoring and explicit geometry checks. For ultralarge libraries (>1M), library… …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-virtual-screening@sha256:6976ad18d658f237The 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_k3ax7zmtywlptouq)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Aug 21, 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 (24500 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
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_k3ax7zmtywlptouq GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-virtual-screening GET https://markdownregistry.com/api/v1/blob/6976ad18d658f237b32c602147636a4d5f20d28f29cdb542aa71fefdc61930e5
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.