GitHub Deep Research
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Predict small-molecule binding poses with DiffDock-L (Corso et al.
Install Diffdock
$ npx skills add JimLiu/science-skills --skill diffdock -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install JimLiu/science-skills diffdock --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/JimLiu/science-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/diffdock .claude/skills/diffdock && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "diffdock" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/diffdock into .claude/skills/diffdock/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "diffdock", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/JimLiu/science-skills/tree/main/skills/diffdockType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add JimLiu/science-skills --skill diffdock -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install JimLiu/science-skills diffdock --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JimLiu/science-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/diffdock .agents/skills/diffdock && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "diffdock" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/diffdock into .agents/skills/diffdock/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "diffdock", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add JimLiu/science-skills --skill diffdock -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install JimLiu/science-skills diffdock --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JimLiu/science-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/diffdock .cursor/skills/diffdock && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "diffdock" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/diffdock into .cursor/skills/diffdock/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "diffdock", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/JimLiu/science-skills.git --path skills/diffdock--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add JimLiu/science-skills --skill diffdock -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install JimLiu/science-skills diffdock --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JimLiu/science-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/diffdock .gemini/skills/diffdock && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "diffdock" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/diffdock into .gemini/skills/diffdock/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "diffdock", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install JimLiu/science-skills diffdockInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add JimLiu/science-skills --skill diffdock -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/JimLiu/science-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/diffdock .github/skills/diffdock && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "diffdock" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/diffdock into .github/skills/diffdock/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "diffdock", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add JimLiu/science-skills --skill diffdock -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install JimLiu/science-skills diffdock --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JimLiu/science-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/diffdock .opencode/skills/diffdock && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "diffdock" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/diffdock into .opencode/skills/diffdock/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "diffdock", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
diffdock- GitHub stars
- 227
- Used in
- 4 other repos
- Token cost
- ~1.1k tokens
- SKILL.md length
- 483 words
- Files
- 2 (incl. references)
- Skills in repo
- 27
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Predict small-molecule binding poses with DiffDock-L (Corso et al.
- Tasks that involve Drug discovery and cheminformatics
- SKILL.md covers Running it, The YAML config overwrites…, The first run is silent for… and The README's --ligand works on…, plus 1 more section
- Calls python3
What it does
Diffdock is an agent skill from JimLiu/science-skills. 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.
Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files, including reference files (for example `references/workflows.md`).
It sits in Research & Science, covering Drug discovery and cheminformatics. It works with GitHub. The licence is Apache-2.0.
When your agent uses it
- Tasks that involve Drug discovery and cheminformatics
Example prompts
- “/diffdock”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit fb309c3. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
python3
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Diffdock loads about 1.1k tokens when it runs, and up to ~1.6k if it reads all its reference files. Until then it costs about 121 tokens; SKILL.md has 483 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from JimLiu/science-skills at commit fb309c3, republished under its Apache-2.0 licence (© JimLiu). 483 words, ~1,113 tokens.
Download SKILL.mdSave it as
.claude/skills/diffdock/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.- name
- diffdock
- description
- 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.
- license
- Apache-2.0
- category
- biomodels
- requirements
- gpu
- metadata.display-name
- DiffDock
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
cd $DIFFDOCK_REPO # a clone of github.com/gcorso/DiffDock
python3 -m inference \
--config default_inference_args.yaml \
--protein_path target.pdb \
--ligand_description "COc1ccc(C#N)cc1" \
--out_dir outFor more than one complex, give --protein_ligand_csv batch.csv instead of the
two single-complex flags; the CSV has four columns — complex_name,
protein_path, ligand_description (SMILES or an .sdf/.mol2 path), and
protein_sequence. Leave protein_path empty and fill protein_sequence to
have DiffDock fold the receptor with ESMFold first; that path and a
larger-library screening recipe are in references/workflows.md.
Under --out_dir/<complex_name>/ each sample is written as
rank{N}_confidence{score}.sdf, plus a copy of rank1.sdf for convenience.
The confidence value in the filename is a logit, so it is unbounded and can be
negative; among samples for the same complex higher is better, but values are
not comparable across different complexes or ligands.
The YAML config overwrites your CLI flags
inference.py loads --config default_inference_args.yaml after argparse
and replaces every key it finds, so passing --samples_per_complex 40 or
--model_dir ... on the command line is silently ignored if the same key sits
in the YAML. To change sampling depth or any other key the YAML defines, copy
the YAML, edit the copy, and point --config at it.
Show full SKILL.md (222 more words)Show less
The first run is silent for ~11 minutes and needs ≥32 GB host RAM
Before the first complex, DiffDock precomputes SO(3) and torus lookup tables.
That step is silent on stderr, takes ~11 minutes, and on the default Modal
tier runs out of host memory and SIGKILLs mid-precompute. Set
provider_params.modal.memory: 65536 (or your provider's equivalent), and do
not assume a hang means a crash.
The README's --ligand works on the CLI by accident — use --ligand_description
The upstream README shows --ligand, which only works because argparse
prefix-matches it to the real flag --ligand_description. That shortcut is
CLI-only: as a CSV column header or YAML key, ligand matches nothing and the
row is silently treated as having no ligand. Spell the flag and the column
header out in full.
Errors worth recognizing
| You see | It means / do this |
|---|---|
ValueError: not allowed to raise maximum limit at startup | setrlimit(NOFILE, 64000) exceeds the sandbox hard limit — sed the constant in inference.py to min(64000, rlimit[1]). |
| Silent SIGKILL a few minutes into the SO(3) precompute | Host RAM exhausted — see the gotcha above. |
python3: not found | You are on the upstream rbgcsail/diffdock image — that one runs from /home/appuser/DiffDock under micromamba. |
Next: rescore the rank1.sdf poses before ranking ligands against each
other — boltz's affinity head is the in-tree option — since the DiffDock
confidence head alone is not an affinity predictor.
© JimLiu, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 1 other file (references) in skills/diffdock of JimLiu/science-skills.
- SKILL.md
- references/workflows.md
Open the folder on GitHubat commit fb309c3
Used in 4 other repositories
We found 4 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 4 other GitHub owners. This page covers the copy in JimLiu/science-skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Diffdock next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Diffdock this skillJimLiu/science-skills | 227 | 4 repos | ~1.1k | Automated safety check: Pass | Apache-2.0 | |
| GitHub Deep Researchbytedance/deer-flow | 83k | 5 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Rival Search MCPdamionrashford/RivalSearchMCP | 132 | 1 repos | ~796 | Automated safety check: Pass | MIT | |
| MolecodeAtomFlow-AI/MoleCode | 305 | — | ~1.9k | Automated safety check: Pass | MIT | |
| Read GitHubAgentTeam-TaichuAI/ScienceClaw | 670 | 2 repos | ~638 | Automated safety check: Pass | None | |
| Drug DiscoveryTommy-yw/RunbookHermes | 546 | 1 repos | ~2.3k | Automated safety check: Pass | MIT |
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Molecode
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A skill your agent uses for deterministic molecule understanding, graph-level editing, generation, and validation with MoleCode — an explicit Mermaid graph in which every atom and bond is a typed…
Read GitHub
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Read and search GitHub repository documentation via gitmcp.io MCP service.
Drug Discovery
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Pharmaceutical research assistant for drug discovery workflows.
DiffDock Molecular Docking
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Predicts how small molecules bind to a protein with DiffDock, covering batch docking, pose ranking by confidence and checks on the results; not for binding affinity.
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Related
Works with
Categories
Questions about Diffdock
What does Diffdock do?
Predict small-molecule binding poses with DiffDock-L (Corso et al. Diffdock is an agent skill from JimLiu/science-skills. Predict small-molecule binding poses with DiffDock-L (Corso et al.
When should I use Diffdock?
Diffdock fits situations like: tasks that involve Drug discovery and cheminformatics.
How do I install Diffdock in Claude Code?
Run `npx skills add JimLiu/science-skills --skill diffdock -a claude-code`. Or copy the skill folder (skills/diffdock in JimLiu/science-skills) into .claude/skills/diffdock in your project. Claude Code loads it when a task matches its description.
How do I install Diffdock in Codex?
Run `npx skills add JimLiu/science-skills --skill diffdock -a codex`. Or copy the skill folder (skills/diffdock in JimLiu/science-skills) into .agents/skills/diffdock in your project. Codex loads it when a task matches its description.
Can I use Diffdock in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add JimLiu/science-skills --skill diffdock -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/diffdock, .gemini/skills/diffdock, .github/skills/diffdock and .opencode/skills/diffdock in your project.
What does Diffdock need to run?
Going by SKILL.md and its folder, Diffdock needs the command-line tools its instructions call (python3). Our summary lists: Python 3.
Does Diffdock access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Diffdock safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Diffdock use?
Diffdock is published under the Apache-2.0 licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Diffdock use?
About 1.1k tokens (SKILL.md is roughly 4.5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 496 tokens, read only when the agent opens those files.
What are the alternatives to Diffdock?
Skills that share tags, products or a category with Diffdock: GitHub Deep Research (bytedance/deer-flow, 83k stars), Rival Search MCP (damionrashford/RivalSearchMCP, 132 stars), Molecode (AtomFlow-AI/MoleCode, 305 stars) and Read GitHub (AgentTeam-TaichuAI/ScienceClaw, 670 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Diffdock?
JimLiu (a GitHub user) maintains it in JimLiu/science-skills, which has 227 GitHub stars. The repository holds 27 skills in this directory. The repository was last updated on July 1, 2026.
Source: JimLiu/science-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.