agentmods.dev

protein-structure-prediction

protein-structure-prediction is a skill for Claude Code from Team-yPark/skills. It costs 155 tokens per session (1,517 once invoked), scanned B, original, Unlicense.

A workflow for predicting and examining a protein's three-dimensional shape from its amino-acid sequence, the chain of building blocks that makes up a protein.

In plain words
What is it for?
Use it to find known structures, choose a suitable prediction model, obtain a structure, and interpret confidence results.
Why use it?
It first checks whether an experimental or existing predicted structure is available, avoiding unnecessary prediction work.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin.

Part of the bcbb-skills plugin — 5 skills shipped together

not rated 2repo 3mo ago B scan 155 tokens original Unlicense

Good fit Use it to find known structures, choose a suitable prediction model, obtain a structure, and interpret confidence results.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/team-ypark/skills/protein-structure-prediction
View source ↗ Team-yPark/skills
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 Team-yPark/skills --skill protein-structure-prediction
Clone the repo
git clone --depth 1 https://github.com/Team-yPark/skills

Made for: Claude Code.

Or install bcbb-skills, the plugin that ships this one along with the rest of its 5 skills.

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 protein-structure-prediction

README.md
[![agentmods](https://agentmods.dev/badge/skills/team-ypark/skills/protein-structure-prediction/github.svg)](https://agentmods.dev/skills/team-ypark/skills/protein-structure-prediction)
Your own site
<a href="https://agentmods.dev/skills/team-ypark/skills/protein-structure-prediction"><img src="https://agentmods.dev/badge/skills/team-ypark/skills/protein-structure-prediction/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 protein-structure-prediction

Your own site · 80×15
<a href="https://agentmods.dev/skills/team-ypark/skills/protein-structure-prediction"><img src="https://agentmods.dev/badge/skills/team-ypark/skills/protein-structure-prediction.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 155 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,517 The whole file, excluding the scripts and references it only reads on demand.
Security scan B 2 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 $0.00155 $0.01517
Opus 5.5 $0.00062 $0.00607
Sonnet 5.5 $0.00031 $0.00303
Haiku 4.5 $0.00015 $0.00152

Measured 2mo ago against content hash beeb1891b5f8, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade B, and why

protein-structure-prediction scanned grade B with 2 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 2mo 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.

Sends data to an external URLmediumData exfiltration

A POST to an outside endpoint may be telemetry or may be exfiltration; either way the mod talks to somewhere, and you should know where.

curl -X POST --data "<AA_SEQUENCE>" https://api.esmatlas.com/foldSequence/v1/pdb/ > pred.pdb

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

curl -X POST --data "<AA_SEQUENCE>" https://api.esmatlas.com/foldSequence/v1/pdb/ > pred.pdb
skills/protein-structure-prediction/SKILL.md · 113 lines

How it starts

The opening of the file, as written. The whole thing — 113 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Protein Structure Prediction from Sequence

Turn an amino-acid sequence into a usable 3D structure: pick a model for the job, obtain the structure (look it up before predicting), and interpret it through its confidence scores. Background biochemistry and model facts live in the knowledge base (be-domain-expert, biochemistry/ and bioinformatics/protein-structure/); this skill is the practical how-to.

First: does the structure already exist?

Predicting is often unnecessary. Check, in order:

  1. PDB (rcsb.org) — an experimental structure (X-ray/cryo-EM/NMR) beats a prediction; search by sequence (BLAST) or ID.
  2. AlphaFold DB (alphafold.ebi.ac.uk) — 200M+ precomputed AF2 models, keyed by UniProt accession. If your protein is there, download it (.pdb + PAE JSON) instead of re-running.
  3. ESM Metagenomic Atlas — for metagenomic/orphan sequences.

Only predict when there is no suitable existing model, the sequence is novel (variant, designed, chimera), or you need a complex/ligand state not in a DB.

Choose the model

Situation Use Why
Single protein, has homologs (deep MSA) ColabFold / AlphaFold2 highest single-chain accuracy
Protein complex (multi-chain), or with DNA/RNA/ligand/ion AlphaFold3 or Boltz model the whole assembly, not lone chains
Open/local complex + ligand, at scale Boltz (Boltz-1/2) open-source AF3-class; runs locally
Many sequences / need speed / orphan or designed protein ESMFold no MSA, ~10× faster, better on shallow-MSA
Just a quick single fold, no setup ESMFold API or ColabFold notebook zero install

Decision rationale (MSA depth, complexes, speed/accuracy trade-offs) is in the knowledge base — consult be-domain-expert if unsure which applies.

Get a structure

Prefer a hosted notebook/API for one-offs; local install for batches.

ColabFold (AF2, MSA via MMseqs2) — the standard accessible AF2:

# local: github.com/sokrypton/ColabFold  (needs GPU + colabfold_batch)
colabfold_batch input.fasta out_dir/    # FASTA: one record per chain
#   complex: put chains in one record separated by ':'  (SEQ1:SEQ2)

Read the full file on GitHub · 113 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. 2mo ago First seen · 113 lines · 155 tokens per session scan B beeb1891b5f8

Subscribe to this mod's changes

protein-structure-prediction is a skill published in the GitHub repository Team-yPark/skills (2 stars, last pushed 3mo ago), licensed Unlicense. It adds 155 tokens to every session and 1,517 once invoked, about $0.0006 per session on Opus 5.5. A static security scan graded it B with 2 findings (sends data to an external url, makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

Scientific
Related

protein-structure-prediction compared with skills from other repositories

protein-structure-prediction next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
protein-structure-predictionTeam-yPark/skillsSkill23mo agoUnlicenseB155Claude Code
instrument-data-to-allotropeanthropics/knowledge-work-pluginsSkill35k3d agoApache-2.0A123Claude Code
exploratory-data-analysisK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA83Claude Code
matlabK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA44Claude Code
phylogeneticsK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA71Claude Code, Codex
research-engineerdavila7/claude-code-templatesSkill33kyesterdayMITA43Claude Code, Codex
mapping-to-snomedmaziyarpanahi/openmedSkill5.8kyesterdayApache-2.0A205Claude Code