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 AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-esmgit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-SkillsWrote 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/alterlab-ieu/alterlab-academic-skills/alterlab-esm)<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-esm"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-esm/github.svg" alt="Measured on agentmods" height="20"></a>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.
<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-esm"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-esm.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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 | $0.00101 | $0.03642 |
| Opus 5.5 | $0.00040 | $0.01457 |
| Sonnet 5.5 | $0.00020 | $0.00728 |
| Haiku 4.5 | $0.00010 | $0.00364 |
Grade A, and why
alterlab-esm 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 1mo 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 — 369 lines — stays where its author put it; the contents beside it link to each section on GitHub.
ESM: Evolutionary Scale Modeling
Overview
ESM provides state-of-the-art protein language models for understanding, generating, and designing proteins. Three families ship in the same esm package:
- ESMC — the current representation model (300M / 600M open weights, 6B via the hosted platform), used for embeddings, logits, and downstream ML features.
- ESMFold2 — structure prediction built on ESMC-6B, hosted via
esmfold2_client. - ESM3 — the generative multimodal model over sequence / structure / function tracks.
Naming and hosting changed — read this before copying old code
EvolutionaryScale now operates as Biohub. The practical consequences:
- The hosted API moved from
forge.evolutionaryscale.aitohttps://biohub.ai; every client inesm.sdkdefaults to that URL and reads the token fromESM_API_KEY. The classes are still named*ForgeInferenceClientfor backwards compatibility. - Model weights live under the
biohubHugging Face organisation (biohub/ESMC-6B,biohub/esm3-sm-open-v1,biohub/ESMFold2). - ESMC and ESMFold2 are also available through Hugging Face Transformers v5.16+, which is
a different dependency stack from the
esmpackage's optimized inference path.
When to Use This Skill
Use this skill when the user wants protein embeddings or logits, a protein structure from an ESM model, inverse folding, or generative sequence design.
Does NOT Trigger
| Scenario | Use Instead |
|---|---|
| Fold a protein or complex with AlphaFold2/ColabFold | alterlab-alphafold |
| Co-fold with a ligand, or predict binding affinity | alterlab-boltz |
| Antibody–antigen or mixed multi-entity complexes | alterlab-chai |
| Design a sequence for a fixed backbone (ProteinMPNN family) | alterlab-proteinmpnn, alterlab-ligandmpnn |
| Generate a de-novo backbone to design onto | alterlab-rfdiffusion |
Core Capabilities
1. Protein Sequence Generation with ESM3
Generate novel protein sequences with desired properties using multimodal generative modeling.
What ships with it
5 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.
- 1mo ago Changed · +59 lines · +12 tokens per session c11fc58f0750
- 1mo ago First seen · 310 lines · 89 tokens per session scan A de97f8d41713
alterlab-esm is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (78 stars, last pushed 4d ago), licensed MIT. It adds 101 tokens to every session and 3,642 once invoked, about $0.0004 per session on Opus 5.5. 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.
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