Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add naity/FM4Life --skill prostt5git clone --depth 1 https://github.com/naity/FM4LifeWrote 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.
[](https://agentmods.dev/skills/naity/fm4life/prostt5)<a href="https://agentmods.dev/skills/naity/fm4life/prostt5"><img src="https://agentmods.dev/badge/skills/naity/fm4life/prostt5.svg" alt="Measured on agentmods" height="20"></a>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.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00141 | $0.02229 |
| Opus 5 | $0.00071 | $0.01115 |
| Sonnet 5 | $0.00028 | $0.00446 |
| Haiku 4.5 | $0.00014 | $0.00223 |
Grade A, and why
prostt5 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 7d 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.
How it starts
The opening of the file, as written. The whole thing — 222 lines — stays where its author put it; the contents beside it link to each section on GitHub.
ProstT5: Protein Sequence ↔ Structure Translation
Overview
ProstT5 is a T5-based protein language model finetuned from ProtT5-XL-U50 to translate between amino acid (AA) sequences and 3Di structural alphabet tokens — the same discrete structural tokens used by Foldseek for fast structure search.
Key capabilities:
- AA → 3Di ("folding"): predict structure as a 3Di string from sequence alone
- 3Di → AA ("inverse folding"): recover amino acid sequences from 3Di structure strings
- Embeddings: high-quality per-residue representations for both AA and 3Di sequences
What 3Di tokens are: Foldseek encodes protein structure as a 20-letter structural alphabet (one token per residue). This is not 3D coordinates — it's a compact structural language. It enables fast structure-based search and comparison without full coordinate files.
When to use ProstT5 vs ESMFold/ESM3:
- ProstT5 outputs 3Di tokens (useful for Foldseek search, structural alphabet analysis)
- ESMFold/ESM3 outputs 3D coordinates (PDB format, for visualization, MD simulation, etc.)
Installation
pip install transformers torch sentencepiece
Model
| HF ID | Notes |
|---|---|
Rostlab/ProstT5 |
Full precision |
Rostlab/ProstT5_fp16 |
Half-precision variant (faster, recommended for GPU) |
Critical Preprocessing Rules
ProstT5 uses a shared tokenizer for both AA and 3Di sequences:
| Sequence type | Format | Prefix token |
|---|---|---|
| Amino acids | UPPERCASE, space-separated, UZOB→X | <AA2fold> |
| 3Di tokens | lowercase, space-separated | <fold2AA> |
The prefix token tells the model which direction to translate. It is required — omitting it produces wrong outputs.
import re
def preprocess_aa(sequence: str) -> str:
"""Prepare an amino acid sequence for ProstT5."""
sequence = re.sub(r"[UZOB]", "X", sequence.upper())
return "<AA2fold> " + " ".join(list(sequence))
def preprocess_3di(structure: str) -> str:
"""Prepare a 3Di sequence for ProstT5."""
return "<fold2AA> " + " ".join(list(structure.lower()))
What ships with it
2 files 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.
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.
- 7d ago First seen · 222 lines · 0 tokens per session scan A e7c04ee02f76
prostt5 is a skill published in the GitHub repository naity/FM4Life (2 stars, last pushed 5mo ago), licensed MIT. It adds 141 tokens to every session and 2,229 once invoked, about $0.0007 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 2026-08-31.
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