GitHub Deep Research
bytedance/deer-flow
Researches a GitHub repository over four rounds using the GitHub API and web search, then writes a structured markdown report with timeline, metrics and Mermaid diagrams.
Inverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al.
Install Ligandmpnn
$ npx skills add JimLiu/science-skills --skill ligandmpnn -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install JimLiu/science-skills ligandmpnn --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/ligandmpnn .claude/skills/ligandmpnn && 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 "ligandmpnn" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/ligandmpnn into .claude/skills/ligandmpnn/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ligandmpnn", 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/ligandmpnnType 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 ligandmpnn -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install JimLiu/science-skills ligandmpnn --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/ligandmpnn .agents/skills/ligandmpnn && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "ligandmpnn" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/ligandmpnn into .agents/skills/ligandmpnn/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ligandmpnn", 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 ligandmpnn -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install JimLiu/science-skills ligandmpnn --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/ligandmpnn .cursor/skills/ligandmpnn && 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 "ligandmpnn" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/ligandmpnn into .cursor/skills/ligandmpnn/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ligandmpnn", 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/ligandmpnn--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 ligandmpnn -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install JimLiu/science-skills ligandmpnn --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/ligandmpnn .gemini/skills/ligandmpnn && 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 "ligandmpnn" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/ligandmpnn into .gemini/skills/ligandmpnn/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ligandmpnn", 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 ligandmpnnInstalls 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 ligandmpnn -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/ligandmpnn .github/skills/ligandmpnn && 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 "ligandmpnn" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/ligandmpnn into .github/skills/ligandmpnn/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ligandmpnn", 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 ligandmpnn -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 ligandmpnn --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/ligandmpnn .opencode/skills/ligandmpnn && 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 "ligandmpnn" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/ligandmpnn into .opencode/skills/ligandmpnn/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ligandmpnn", 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
ligandmpnn- GitHub stars
- 228
- Used in
- 4 other repos
- Token cost
- ~1.5k tokens
- SKILL.md length
- 653 words
- Files
- 1
- Skills in repo
- 27
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Inverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al.
- Research & Science work in your project
- SKILL.md covers Running it, Model types — which one to pick, ProDy compiles from source on… and Turning ligand context off…, plus 2 more sections
- Calls pip, bash and git; reaches github.com
What it does
Ligandmpnn is an agent skill from JimLiu/science-skills. Inverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al. 2023, github.com/dauparas/LigandMPNN). Reach for this skill to redesign the residues lining a binding pocket around a bound small molecule or cofactor, to design metal-coordinating sites where the geometry must be respected, or to get threaded designed-sequence PDBs out of any MPNN run.
Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science. It works with GitHub. The licence is Apache-2.0.
When your agent uses it
- Research & Science work in your project
Example prompts
- “/ligandmpnn”
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:
pipbashgitpython
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
github.com
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
Ligandmpnn loads about 1.5k tokens when it runs. Until then it costs about 100 tokens; SKILL.md has 653 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). 653 words, ~1,546 tokens.
Download SKILL.mdSave it as
.claude/skills/ligandmpnn/SKILL.md (or your agent's skills folder).- name
- ligandmpnn
- description
- Inverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al. 2023, github.com/dauparas/LigandMPNN). Reach for this skill to redesign the residues lining a binding pocket around a bound small molecule or cofactor, to design metal-coordinating sites where the geometry must be respected, or to get threaded designed-sequence PDBs out of any MPNN run.
- license
- Apache-2.0
- category
- biomodels
- metadata.display-name
- LigandMPNN
LigandMPNN
LigandMPNN extends the ProteinMPNN graph with non-protein atoms — small
molecules, nucleic acids, and metals are visible to the network — so it is the
right inverse-folding tool whenever the design surface includes a bound ligand
or cofactor that vanilla proteinmpnn would ignore. The same run.py is also
the most convenient runner for the other MPNN families because, unlike the
original ProteinMPNN script, it threads designs back onto the input structure
and writes PDBs alongside the FASTA. Code and weights are MIT
(github.com/dauparas/LigandMPNN). The model is small enough to run on CPU —
for a handful of designs on one structure that is seconds and usually faster
than dispatching, so the normal path is local with
pip install torch numpy biopython ProDy ml_collections dm-tree; a GPU helps
for batched campaigns.
Running it
pip install torch numpy biopython ProDy ml_collections dm-tree
git clone --depth 1 https://github.com/dauparas/LigandMPNN.git ligandmpnn
cd ligandmpnn
sed -i 's/np\.int\b/np.int64/g' openfold/np/residue_constants.py # repo pins numpy 1.23; alias removed in >=1.24
bash get_model_params.sh ./model_params
python run.py \
--model_type ligand_mpnn \
--checkpoint_ligand_mpnn ./model_params/ligandmpnn_v_32_010_25.pt \
--pdb_path complex.pdb \
--out_folder out \
--batch_size 8 --number_of_batches 4 \
--temperature 0.1 \
--fixed_residues "A45 A46 A47 A48"Residue selections are space-separated {chain}{resnum} tokens inside one
quoted string ("A45 A46 B10"; insertion codes append directly, "B82A").
That is the format for --fixed_residues and --redesigned_residues;
--bias_AA_per_residue and --omit_AA_per_residue instead take a path to a
JSON file whose keys use the same {chain}{resnum} form, and
--chains_to_design is comma-separated ("A,B"). If you want to redesign only the pocket, naming the pocket residues
in --redesigned_residues is usually shorter than fixing everything else.
Under --out_folder you get seqs/<stem>.fa (headers carry
overall_confidence and ligand_confidence), backbones/<stem>_{1..N}.pdb
with the designed sequence threaded onto the input coordinates, and — with
--pack_side_chains 1 — full-atom packed models in packed/. The threaded
PDBs are the reason to prefer this runner even for protein-only jobs.
Model types — which one to pick
--model_type | sees | use |
|---|---|---|
ligand_mpnn | backbone + ligand/NA/metal atoms | binding-pocket or active-site design |
protein_mpnn | backbone only | protein–protein; same weights as proteinmpnn |
soluble_mpnn | backbone only, soluble-trained | expression-biased prior; see solublempnn |
*_membrane_mpnn | backbone + membrane label | transmembrane designs |
Each model type has its own --checkpoint_<type> flag; the wrong pairing is
caught at load time, but the default checkpoint path is relative to the repo,
so run from inside the clone or pass the absolute path.
ProDy compiles from source on py3.11 — pip install fails without a C compiler
run.py imports ProDy unconditionally for ligand atom parsing. On py3.11 the
prebuilt wheel is missing on PyPI, so pip install ProDy compiles from source
and needs a working C/C++ compiler. On Modal's add_python bases the default
CXX=clang++ points at a missing binary — apt_install("build-essential")
and export CC=gcc CXX=g++ before the install. On most CPU-local Python
distributions the sdist builds in ~10 s if no wheel matches your Python.
Show full SKILL.md (254 more words)Show less
Turning ligand context off changes the answer, not the model
--ligand_mpnn_use_atom_context 0 keeps the ligand-aware weights but masks the
ligand atoms at inference. That is useful for an ablation — the difference
between context-on and context-off tells you how much the ligand is shaping the
design — but it is not equivalent to running protein_mpnn, which uses a
different checkpoint trained without those features. For a fair protein-only
baseline, switch --model_type.
Stripped HETATM or a chain filter silently drops the ligand — the design comes back pocket-blind
LigandMPNN does not warn when no ligand atoms are found; it just runs as if
--model_type protein_mpnn had been picked. The two common ways this happens
are an input PDB whose HETATM records were stripped by an upstream
clean-up step, and --parse_these_chains_only naming the protein chains but
not the ligand's. If ligand_confidence in the FASTA header is missing or
zero across every design, the model never saw the ligand — fix the input, do
not trust the sequences.
Errors worth recognizing
| You see | It means / do this |
|---|---|
ModuleNotFoundError: No module named 'tree' | pip install dm-tree — the vendored openfold imports it unconditionally. |
module 'numpy' has no attribute 'int' | Run the sed patch on openfold/np/residue_constants.py, or pin numpy<1.24 (py≤3.11 only). |
error: command 'clang' failed while pip install ProDy | See the ProDy gotcha above — apt_install("build-essential") and env({"CC":"gcc","CXX":"g++"}). |
FileNotFoundError for model_params/... | Checkpoints not fetched — run bash get_model_params.sh ./model_params from inside the clone. |
Next: fold the designs in complex with the ligand via boltz or chai1
(both accept SMILES/CCD) and filter on ipTM and ligand placement.
© 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
Just SKILL.md in skills/ligandmpnn of JimLiu/science-skills.
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
Ligandmpnn 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 |
|---|---|---|---|---|---|---|
| Ligandmpnn this skillJimLiu/science-skills | 228 | 4 repos | ~1.5k | Automated safety check: Pass | Apache-2.0 | |
| GitHub Deep Researchbytedance/deer-flow | 84k | 4 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Last30daysmvanhorn/last30days-skill | 64k | — | ~7.9k | Automated safety check: Notes | MIT | |
| Read GitHubAgentTeam-TaichuAI/ScienceClaw | 671 | 2 repos | ~638 | Automated safety check: Pass | None | |
| Ideer Daily PaperAI45Lab/iDeer | 416 | — | ~2.3k | Automated safety check: Notes | AGPL-3.0 | |
| Rival Search MCPdamionrashford/RivalSearchMCP | 132 | — | ~796 | Automated safety check: Pass | MIT |
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Related
Works with
Categories
Questions about Ligandmpnn
What does Ligandmpnn do?
Inverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al. Ligandmpnn is an agent skill from JimLiu/science-skills. Inverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al.
When should I use Ligandmpnn?
Ligandmpnn fits situations like: research & Science work in your project.
How do I install Ligandmpnn in Claude Code?
Run `npx skills add JimLiu/science-skills --skill ligandmpnn -a claude-code`. Or copy the skill folder (skills/ligandmpnn in JimLiu/science-skills) into .claude/skills/ligandmpnn in your project. Claude Code loads it when a task matches its description.
How do I install Ligandmpnn in Codex?
Run `npx skills add JimLiu/science-skills --skill ligandmpnn -a codex`. Or copy the skill folder (skills/ligandmpnn in JimLiu/science-skills) into .agents/skills/ligandmpnn in your project. Codex loads it when a task matches its description.
Can I use Ligandmpnn 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 ligandmpnn -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/ligandmpnn, .gemini/skills/ligandmpnn, .github/skills/ligandmpnn and .opencode/skills/ligandmpnn in your project.
What does Ligandmpnn need to run?
Going by SKILL.md and its folder, Ligandmpnn needs the command-line tools its instructions call (pip, bash, git and python). Our summary lists: Python 3.
Does Ligandmpnn access the network?
SKILL.md names 1 domain. In commands or code: github.com; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.
Is Ligandmpnn 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 Ligandmpnn use?
Ligandmpnn 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 Ligandmpnn use?
About 1.5k tokens (SKILL.md is roughly 6.2k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Ligandmpnn?
Skills that share tags, products or a category with Ligandmpnn: GitHub Deep Research (bytedance/deer-flow, 84k stars), Last30days (mvanhorn/last30days-skill, 64k stars), Read GitHub (AgentTeam-TaichuAI/ScienceClaw, 671 stars) and Ideer Daily Paper (AI45Lab/iDeer, 416 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Ligandmpnn?
JimLiu (a GitHub user) maintains it in JimLiu/science-skills, which has 228 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.