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solublempnn

solublempnn is a skill for Claude Code, Codex from zongtingwei/Bioclaw_Skills_Hub. It costs 91 tokens per session (1,448 once invoked), scanned A, original, MIT.

A protein-design workflow that uses SolubleMPNN to suggest protein sequences intended to dissolve better in water. It is aimed at proteins designed for production in E. coli bacteria.

In plain words
What is it for?
Use it to generate sequences from a protein backbone structure, optimize solubility, reduce aggregation risk, and support higher-yield E. coli expression.
Why use it?
It addresses aggregation and insoluble expression, where a designed protein clumps or forms deposits instead of being produced in a usable form.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one. Also seen: positional $N argument.

Needs its repository: it reads a path above its own folder, which exists only inside the repository. The line is **First time?** See [Installation Guide](../../docs/installation.md) to set up Modal and biomodals..

not rated 26repo 5mo ago A scan 91 tokens original MIT

Good fit Use it to generate sequences from a protein backbone structure, optimize solubility, reduce aggregation risk, and support higher-yield E. coli expression.

Compare 6 skills from other repositories ↓
View source ↗ zongtingwei/Bioclaw_Skills_Hub
Install

Getting it into your agent

It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.

Clone the repo
git clone --depth 1 https://github.com/zongtingwei/Bioclaw_Skills_Hub
agentmods
npx agentmods add skills/zongtingwei/bioclaw_skills_hub/solublempnn

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for solublempnn

README.md
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Your own site
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Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for solublempnn

Your own site · 80×15
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Per session 91 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,448 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00091 $0.01448
Opus 5 $0.00046 $0.00724
Sonnet 5 $0.00018 $0.00290
Haiku 4.5 $0.00009 $0.00145

Measured 12d ago against content hash c2dcf58c291d, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

solublempnn scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/protein-design/skills/solublempnn/SKILL.md · 182 lines

How it starts

The opening of the file, as written. The whole thing — 182 lines — stays where its author put it; the contents beside it link to each section on GitHub.

SolubleMPNN Solubility-Optimized Design

Prerequisites

Requirement Minimum Recommended
Python 3.8+ 3.10
CUDA 11.0+ 11.7+
GPU VRAM 8GB 16GB (T4)
RAM 8GB 16GB

How to run

First time? See Installation Guide to set up Modal and biomodals.

Option 1: Modal (recommended)

SolubleMPNN uses the ProteinMPNN Modal wrapper with soluble model:

cd biomodals
modal run modal_proteinmpnn.py \
  --pdb-path backbone.pdb \
  --num-seq-per-target 16 \
  --sampling-temp 0.1 \
  --model-name v_48_020

GPU: T4 (16GB) | Timeout: 600s default

Option 2: Local installation

git clone https://github.com/dauparas/ProteinMPNN.git
cd ProteinMPNN

# Use soluble model weights
python protein_mpnn_run.py \
  --pdb_path backbone.pdb \
  --out_folder output/ \
  --num_seq_per_target 16 \
  --sampling_temp "0.1" \
  --model_name "v_48_020"  # Soluble model

Key parameters

Parameter Default Range Description
--pdb_path required path Input structure
--num_seq_per_target 1 1-1000 Sequences per structure
--sampling_temp "0.1" "0.0001-1.0" Temperature (string!)
--model_name v_48_020 string Soluble model variant

Model Variants

Model Description Use Case
v_48_002 Standard General design
v_48_020 Soluble-trained E. coli expression
v_48_030 High solubility Difficult targets

Output format

output/
├── seqs/backbone.fa
└── backbone_pdb/backbone_0001.pdb

Sample output

Successful run

$ python protein_mpnn_run.py --pdb_path backbone.pdb --model_name v_48_020 --num_seq_per_target 8
Loading soluble model weights (v_48_020)...
Designing sequences for backbone.pdb
Generated 8 sequences in 2.1 seconds

output/seqs/backbone.fa:
>backbone_0001, score=1.31, global_score=1.24, seq_recovery=0.78
MKTAYIAKQRQISFVKSHFSRQLE...
>backbone_0002, score=1.28, global_score=1.21, seq_recovery=0.81
MKTAYIAKQRQISFVKSQFSRQLD...

Read the full file on GitHub · 182 lines

Files

What ships with it

1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 12d ago First seen · 182 lines · 91 tokens per session scan A c2dcf58c291d

Subscribe to this mod's changes

solublempnn is a skill published in the GitHub repository zongtingwei/Bioclaw_Skills_Hub (26 stars, last pushed 5mo ago), licensed MIT. It adds 91 tokens to every session and 1,448 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Scientificagentbioinformaticsdesign-toolsinverse-foldingopenclawsequence-designskillssolubility
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