What is bio-alignment-structural?

A guide to comparing the three-dimensional shapes of proteins. It uses structure comparisons to find similar folds when comparing their amino-acid sequences is not enough.

Use it to align protein structures, find similar structures at scale, create structure-based multiple alignments, and compare predicted models.

Proteins can have related shapes even when their sequences are very different. Structure comparison can uncover remote relationships that sequence alignment misses.

bio-alignment-structural — Skill by PKU-YuanGroup/OpenAI4S

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 PKU-YuanGroup/OpenAI4S --skill bio-alignment-structural-alignment

Clone the repo

git clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4S

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/pku-yuangroup/openai4s/bio-alignment-structural-alignment/github.svg)](https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-structural-alignment)

Your own site

<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-structural-alignment"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-structural-alignment/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/pku-yuangroup/openai4s/bio-alignment-structural-alignment"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-structural-alignment.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 102 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 6,154 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.

Origin 98% copy Near-identical to another mod 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	$0.00102	$0.06154
Opus 5.5	$0.00041	$0.02462
Sonnet 5.5	$0.00020	$0.01231
Haiku 4.5	$0.00010	$0.00615

Measured 1mo ago against content hash e3ddefc217da, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

bio-alignment-structural 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.

The scan reads SKILL.md. This mod also ships 4 executable files (scripts/biopython_superimposer.py, scripts/foldmason_msa.py, scripts/foldseek_search.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

Origin

This is a copy

98% identical to bio-alignment-structural — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

skills/bioskills/bio-alignment-structural-alignment/SKILL.md · 339 lines

How it starts

The opening of the file, as written. The whole thing — 339 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Version Compatibility

Reference examples tested with: Foldseek 8+, TM-align 20220412+, US-align 20231222+, Foldmason 1+, BioPython 1.83+, pymol-open-source 3.0+

Before using code patterns, verify installed versions match. If versions differ:

CLI: foldseek --version, TMalign, USalign, foldmason --version
Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Structural Alignment

"Align two protein structures" -> Compute backbone-aware superposition and a fold-similarity score (TM-score, RMSD, or LDDT).

CLI pairwise: TMalign A.pdb B.pdb, USalign A.pdb B.pdb
CLI search at scale: foldseek easy-search query/ AFDB result.m8 tmp/
CLI structural MSA: foldmason easy-msa structures/*.pdb out tmp/
Python pairwise: Bio.PDB.Superimposer, or subprocess wrapping TMalign / USalign (see examples/tm_align_pairwise.py)
GUI / scripted molecular-graphics superposition: ChimeraX matchmaker, PyMOL super/cealign

"Find structural homologs of an AlphaFold model" -> Search a structure database by 3Di-encoded structural alphabet (Foldseek) or by full TM-align rotation (DALI, US-align).

When to Use Structural Alignment

Sequence identity	Recommended approach
>= 40%	Sequence DP (Bio.Align, BLASTP) is sufficient
25-40%	Sensitive sequence (MMseqs2, jackhmmer, profile-profile HHsearch)
15-25%	Profile-profile (HHsearch) OR Foldseek if structures available
< 15% (dark proteome / twilight zone)	Foldseek (3Di), TM-align, US-align, pLM aligners

Sequence alignment below 15% identity is statistically indistinguishable from random pairings. The exact twilight-zone cutoff is length-dependent: Rost 1999 (Prot Eng) showed the curve drops to 25% at length 80, 20% at length 250 -- short alignments need higher identity for the same statistical signal, so a 15-25% rule of thumb is shorthand for "twilight zone for proteins of typical domain size (~150-300 residues)". If reasonable structural models exist (PDB, AlphaFoldDB, ESMFold), structural alignment is far more reliable in this regime.

Read the full file on GitHub · 339 lines

Files

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.

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.

1mo ago First seen · 339 lines · 102 tokens per session scan A e3ddefc217da

Subscribe to this mod's changes

bio-alignment-structural is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (626 stars, last pushed yesterday), licensed MIT. It adds 102 tokens to every session and 6,154 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it A with 0 findings. It is 98% identical to bio-alignment-structural, differing in 12 lines, and is treated as a copy.

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