A structure-prediction tool for checking how a designed protein folds on its own or when joined to another protein.

Validating protein sequences, predicting protein complexes, and filtering designs before further testing.

It helps test whether a designed sequence is likely to form the intended structure and provides confidence scores for the prediction.

foldseek — Skill for Claude Code and Codex by zongtingwei

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 zongtingwei/Bioclaw_Skills_Hub --skill foldseek

Clone the repo

git clone --depth 1 https://github.com/zongtingwei/Bioclaw_Skills_Hub

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/zongtingwei/bioclaw_skills_hub/foldseek/github.svg)](https://agentmods.dev/skills/zongtingwei/bioclaw_skills_hub/foldseek)

Your own site

<a href="https://agentmods.dev/skills/zongtingwei/bioclaw_skills_hub/foldseek"><img src="https://agentmods.dev/badge/skills/zongtingwei/bioclaw_skills_hub/foldseek/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/zongtingwei/bioclaw_skills_hub/foldseek"><img src="https://agentmods.dev/badge/skills/zongtingwei/bioclaw_skills_hub/foldseek.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 101 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,485 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 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.

Model	Per session	Once invoked
Fable 5.1	$0.00101	$0.01485
Opus 5.5	$0.00040	$0.00594
Sonnet 5.5	$0.00020	$0.00297
Haiku 4.5	$0.00010	$0.00148

Measured 2mo ago against content hash b46ae3860726, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

foldseek scanned grade A 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.

Makes network callslowCapability

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

curl -X POST "https://search.foldseek.com/api/ticket" \

Runs shell commandslowCapability

Expected in a hook, worth knowing in a rule or an instructions file.

subprocess.run([

skills/protein-design/skills/foldseek/SKILL.md · 196 lines

How it starts

The opening of the file, as written. The whole thing — 196 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Foldseek Structure Search

Prerequisites

Requirement	Minimum	Recommended
Python	3.8+	3.10
RAM	8GB	16GB
Disk	10GB	50GB (for local databases)

How to run

Note: Foldseek can run locally or via web server. No GPU required.

Option 1: Web Server (Quick; rate-limited, use sparingly)

# Upload structure to web server
curl -X POST "https://search.foldseek.com/api/ticket" \
  -F "[email protected]" \
  -F "database[]=afdb50" \
  -F "database[]=pdb100"

Option 2: Local installation

# Install Foldseek
conda install -c conda-forge -c bioconda foldseek

# Search PDB
foldseek easy-search query.pdb /path/to/pdb100 results.m8 tmp/

# Search AlphaFold DB
foldseek easy-search query.pdb /path/to/afdb50 results.m8 tmp/

Option 3: Python API

import subprocess
import pandas as pd

def foldseek_search(query_pdb, database, output="results.m8"):
    """Run Foldseek search."""
    subprocess.run([
        "foldseek", "easy-search",
        query_pdb, database, output, "tmp/",
        "--format-output", "query,target,pident,alnlen,evalue,bits"
    ])
    return pd.read_csv(output, sep="\t",
                       names=["query", "target", "pident", "alnlen", "evalue", "bits"])

Key parameters

Parameter	Default	Description
`--min-seq-id`	0.0	Minimum sequence identity
`-e`	0.001	E-value threshold
`--alignment-type`	2	0=3Di, 1=TM, 2=3Di+AA
`--max-seqs`	300	Max hits to pass through prefilter; reducing this affects sensitivity

Databases

Database	Description	Size
`pdb100`	PDB clustered at 100%	~200K structures
`afdb50`	AlphaFold DB at 50%	~67M structures
`swissprot`	SwissProt structures	~500K structures
`cath50`	CATH domains	~50K domains

Output format

# results.m8 (tabular)
query   target          pident  alnlen  evalue  bits
query   1abc_A          85.2    120     1e-45   180.5
query   2def_B          72.1    115     1e-32   145.2

Read the full file on GitHub · 196 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.

README.md 798 B

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.

2mo ago First seen · 196 lines · 101 tokens per session scan A b46ae3860726

Subscribe to this mod's changes

foldseek is a skill published in the GitHub repository zongtingwei/Bioclaw_Skills_Hub (27 stars, last pushed 6mo ago), licensed MIT. It adds 101 tokens to every session and 1,485 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it A with 2 findings (makes network calls, runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Scientific agent bioinformatics openclaw search similarity skills structure utilities

foldseek next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
foldseekzongtingwei/Bioclaw_Skills_Hub	Skill	27	6mo ago	MIT	A	101	Claude Code, Codex
foldseekBioTender-max/awesome-bio-agent-skills	Skill	216	4mo ago	none	A	90	Claude Code, Codex
foldseekadaptyvbio/protein-design-skills	Skill	173	4mo ago	MIT	A	90	Claude Code, Codex
foldseekBioTender-max/ProteinClaw	Skill	11	8mo ago	none	A	90	Claude Code, Codex
academic-paper-to-chinese-insight-pdfdavidtoby/agent-skills	Skill	11	yesterday	MIT	A	0	Claude Code, Codex
chinese-pdf-document-workflowsdavidtoby/agent-skills	Skill	11	yesterday	MIT	A	83	Claude Code, Codex
jupyter-live-kerneldavidtoby/agent-skills	Skill	11	yesterday	MIT	A	19	Claude Code, Codex

foldseek