drug-discovery-pipeline SKILL.md skillA
This file is byte-identical to the first copy the registry indexed, one of 3 indexed copies. Same content hash, so the same checks give both the same grade.
drug-discovery-pipeline from nvidia-bionemo/bionemo-agent-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add nvidia-bionemo/bionemo-agent-toolkit/drug-discovery-pipeline@git:20260825.0e67a61Pins git:20260825.0e67a61 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- nvidia-bionemo/bionemo-agent-toolkit
- Path
skills/bionemo-agent-toolkit/skills/drug-discovery-pipeline/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260825.0e67a61, committed Aug 25, 2026
- Size
- 7,367 bytes
- Repository stars
- 503
- License
- a license file GitHub does not identify
NOTE: molecule and target inputs and your NGC_API_KEY are transmitted to external NVIDIA-hosted API endpoints on every call. Use local NIM containers for confidential or proprietary data. Run a complete computational drug discovery pipeline using NVIDIA BioNeMo NIMs: generate drug-like molecules with GenMol, dock them to a protein target with DiffDock, then predict binding affinity with Boltz2. Use this skill whenever the user wants to generate and screen small molecule drug candidates…
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
# Drug Discovery Pipeline Screen drug candidates end-to-end using three BioNeMo NIMs in sequence: ``` Step 1: GenMol → Step 2: DiffDock → Step 3: Boltz2 (Generate mols) (Dock to target) (Predict affinity) ``` --- ## Overview This pipeline is used for: - **De novo hit discovery**: generate drug-like molecules and screen them against a target - **Lead optimization**: start from a known scaffold and generate improved analogs, then dock and score - **Virtual screening**: dock a library of candidates and filter by docking confidence + affinity --- ## Before you start Confirm with the user: 1. **Target protein**: PDB file or sequence of the binding target 2. **Starting point**: de novo (no scaffold) or scaffold decoration (known core)? 3. **Scoring**: drug-likeness (QED) or lipophilicity (LogP)? 4. **API mode**: hosted or local Docker? For local Docker, do not assume all NIMs are running on `localhost:8000` at the same time. Either run one container at a time and hand files/results between steps, or start each NIM on a distinct host port and set the per-step URLs. --- ## Step 1: Generate molecules with GenMol …
Read the whole file at its exact version.
How to install
mdr add nvidia-bionemo/bionemo-agent-toolkit/drug-discovery-pipeline@sha256:15a8d2235a8d01a3The line at the top of this page pins the label git:20260825.0e67a61, 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_tu7tqwgebp3cxq7j)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Aug 25, 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 (7367 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
nvidia-bionemo/bionemo-agent-toolkit · 503 stars · license a license file GitHub does not identify · pushed 2026-11-05 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_tu7tqwgebp3cxq7j GET https://markdownregistry.com/api/v1/resolve?ref=nvidia-bionemo/bionemo-agent-toolkit/drug-discovery-pipeline GET https://markdownregistry.com/api/v1/blob/15a8d2235a8d01a306bffc6b19a9db1e7bad0be993c2ff017669b99cc1fecf13
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.
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