esmfold2

esmfold2 is a skill for Claude Code, Codex from companion-inc/feynman. It costs 38 tokens per session (202 once invoked), scanned A, original, MIT.

A workflow for predicting a protein’s three-dimensional shape from its amino-acid sequence. It is designed for quick estimates without using a multiple sequence alignment, a comparison of related sequences.

In plain words
What is it for?
Use it to compare mutations, review uncertain regions, screen protein sequences, and save predicted structure files and confidence results.
Why use it?
It provides an early structural estimate for screening sequences or variants before using slower prediction methods.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

Good fit Use it to compare mutations, review uncertain regions, screen protein sequences, and save predicted structure files and confidence results.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/companion-inc/feynman/esmfold2
About the project

Feynman is an open-source AI research agent that helps users investigate topics with language models. It supports local model providers and hosted model authentication through its setup process. The catalogue contains skills, agents, and instructions that extend Feynman’s workflows.

companion-inc/feynman · 8,870 stars · on GitHub · feynman.is

Install

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.

Any agent
npx skills add companion-inc/feynman --skill esmfold2
Clone the repo
git clone --depth 1 https://github.com/companion-inc/feynman

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 esmfold2

README.md
[![agentmods](https://agentmods.dev/badge/skills/companion-inc/feynman/esmfold2/github.svg)](https://agentmods.dev/skills/companion-inc/feynman/esmfold2)
Your own site
<a href="https://agentmods.dev/skills/companion-inc/feynman/esmfold2"><img src="https://agentmods.dev/badge/skills/companion-inc/feynman/esmfold2/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.

agentmods 80×15 button for esmfold2

Your own site · 80×15
<a href="https://agentmods.dev/skills/companion-inc/feynman/esmfold2"><img src="https://agentmods.dev/badge/skills/companion-inc/feynman/esmfold2.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 38 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 202 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. Third-party audits
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
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 $0.00038 $0.00202
Opus 5 $0.00019 $0.00101
Sonnet 5 $0.00008 $0.00040
Haiku 4.5 $0.00004 $0.00020

Measured 10d ago against content hash 074179a89177, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

esmfold2 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 10d 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/esmfold2/SKILL.md · 19 lines

What it actually says

ESMFold2

Use this skill when a fast protein fold hypothesis is useful before heavier structure prediction.

Workflow:

  1. Normalize sequences into FASTA and record identifiers, mutations, truncations, domains, and oligomer assumptions.
  2. Verify the local or endpoint route before running.
  3. Save FASTA, model version, command or request body, predicted PDB/mmCIF, pLDDT/confidence outputs, and logs.
  4. Flag low-confidence regions, missing multimers, disorder, membrane regions, and sequence lengths outside the chosen route's limits.
  5. Use RDKit/3Dmol/PDB previews and source-backed comparisons when the output influences a research decision.

Use ESMFold-style predictions for triage unless an independent check supports the structural claim.

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. 10d ago First seen · 19 lines · 38 tokens per session scan A 074179a89177

Subscribe to this mod's changes

esmfold2 is a skill published in the GitHub repository companion-inc/feynman (8,870 stars, last pushed 13d ago), licensed MIT. It adds 38 tokens to every session and 202 once invoked, about $0.0002 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.

Related

Other skills, from other repositories

instrument-data-to-allotrope

Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full…

anthropics/knowledge-work-plugins · 123 tokens

exploratory-data-analysis

Perform bounded, local exploratory analysis of explicitly supported scientific files. Use for redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection; missingness/leakage audits; outlier and transformation sensitivity; and rigorous EDA report scaffolds. Other domain…

K-Dense-AI/scientific-agent-skills · 83 tokens

matlab

Build, review, migrate, and safely plan MATLAB or GNU Octave numerical workflows, including arrays, tabular/time data, tests, projects, graphics, MAT files, and explicit Python interoperability.

K-Dense-AI/scientific-agent-skills · 42 tokens

phylogenetics

Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.

K-Dense-AI/scientific-agent-skills · 68 tokens

research-engineer

An uncompromising Academic Research Engineer. Operates with absolute scientific rigor, objective criticism, and zero flair. Focuses on theoretical correctness, formal verification, and optimal implementation across any required technology.

davila7/claude-code-templates · 43 tokens

mapping-to-snomed

Maps clinical concept spans extracted by OpenMed to SNOMED CT concepts through a USER-SUPPLIED terminology server (the user's own Ontoserver, Snowstorm, or UMLS/UTS), never a bundled vocabulary. Use when the user wants to code findings, disorders, procedures, body structures, or substances to SNOMED CT, run an ECL…

maziyarpanahi/openmed · 205 tokens