Individual skill
diffdock
Predict small-molecule binding poses with DiffDock-L (Corso et al. 2023/2024, github.com/gcorso/DiffDock) — blind diffusion docking that places a ligand into a protein pocket without a predefined search box and ranks the samples with a learned confidence model. Reach for this skill to dock a SMILES or SDF against a PDB, to generate ranked 3D poses for a small fragment library, or to get a starting pose for downstream rescoring. DiffDock predicts geometry, not affinity.
configs/microservice/bff-service/configs/agent-skills/claude-science/diffdock/SKILL.md
Source commit 3f908c703fd75033217ed549f1998563d13a1dc0
What was checked
- Matches the observed repository HEAD
- Yes
- Scanner rules are current
- Yes
- Repository scan complete
- No
- Skill scan complete
- No
- Observed behavior
- Network or broad shell
- Last checked
- Nov 9, 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)
- 2,386
- Repository last updated
- Nov 6, 2026
- License
- Apache-2.0
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- ai Repository topic
- llm Repository topic
- mcp Repository topic
- rag Repository topic
- wanwu Repository topic
- workflow Repository topic
- agentic-ai Repository topic
- agentic-framework Repository topic
- ai-agent Repository topic
- ai-agent-development-framework Repository topic
- engineering Derived category
Files and excerpt
File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.
Browse files
.catalog_stampruns · 13 bytesSKILL.mdcore · 4,476 bytesSKILL.mdcore · 4,476 bytesreferences/workflows.mdruns · 1,984 bytes
Read excerpt
# DiffDock-L
DiffDock-L is a blind pose predictor: given a protein structure and a ligand,
it samples ligand placements over the whole surface with a diffusion model and
ranks them with a separately trained confidence head. The confidence score
correlates with pose correctness, not with binding free energy — DiffDock does
not predict whether or how tightly the ligand binds, so for hit triage you
still pair it with a scorer (GNINA, MM-GBSA) or with `boltz`'s affinity head.
For protein–protein and nucleic-acid co-folding, route to `boltz` or `chai1`.
Code and weights are MIT (github.com/gcorso/DiffDock).
## Running it
```bash