ipSAE

ipSAE is an AI Engineering skill for Claude Code, published by BioTender-max in awesome-bio-agent-skills.

174 stars30 forkson BioTender-max/awesome-bio-agent-skillsAdded 2026/09/07+1% in starsRepository updated 2026/07/01

agent-skillsai-agentai-agentsawesomeawesome-listbioinformaticsbiomedicalclaudeclaude-codeclaude-skillscomputational-biologydrug-discoverygenomicsllmmcpprotein-designproteomicssingle-cellskillstranscriptomics

Install in seconds

Install ipSAE

Copy ipSAE into your Claude Code skills folder. Run the command in your terminal, or review the source on GitHub before installing.

terminal

npx degit https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/adaptyv/ipsae ~/.claude/skills/ipsae

Requires Node.js. Downloads this skill only — not the rest of the repository — into your Claude Code skills folder.

Without Node.js

git clone https://github.com/BioTender-max/awesome-bio-agent-skills.git

Clones the whole repository, then copy the skill’s own directory into your skills folder yourself.

In this catalog

Source file: skills/adaptyv/ipsae/SKILL.md in BioTender-max/awesome-bio-agent-skills
Installs to: ~/.claude/skills/ipsae
Collection: One of 25 skills cataloged from this repository
Category: AI Engineering — 3475 skills

What ipSAE does

ipSAE ranks protein binder designs using interprotein Score from Aligned Errors (ipSAE). Use it to filter AF2, AF3, or Boltz predictions and prioritize designs for experimental testing.

ipSAE is cataloged under AI Engineering on DirSkills. ipSAE comes from a repository tagged agent-skills, ai-agent, ai-agents, awesome and awesome-list.

Documentation

README

Excerpt

ipSAE Binder Ranking

Prerequisites

Requirement	Minimum	Recommended
Python	3.8+	3.10
NumPy	1.20+	Latest
RAM	8GB	16GB

Overview

ipSAE (interprotein Score from Aligned Errors) is a scoring function for ranking protein-protein interactions predicted by AlphaFold2, AlphaFold3, and Boltz1. It outperforms ipTM and iPAE for binder design ranking with 1.4x higher precision in identifying true binders.

Paper: What's wrong with AlphaFold's ipTM score

How to run

Installation

git clone https://github.com/DunbrackLab/IPSAE.git
cd IPSAE
pip install numpy

This is the opening of the README. Read the full README on GitHub.

Frequently asked about ipSAE

What else does BioTender-max publish alongside ipSAE?
ipSAE is one of 25 skills that DirSkills catalogs from BioTender-max/awesome-bio-agent-skills, the repository it ships in. Its siblings there include ATAC Seq, AlphaFold and BindCraft Binder Design. Each one is a separate skill with its own page in this directory, installs the same way ipSAE does, and is maintained by BioTender-max in that same repository. The rest of the collection is listed on the BioTender-max/awesome-bio-agent-skills page.
How does ipSAE compare to other AI Engineering skills?
ipSAE ranks #3223 by stars among the 3475 AI Engineering skills in this catalog. The most-starred ones next to it are Architecture Decision Records, AI-First Engineering and Agentic OS. DirSkills ranks by the star count of the repository each skill ships in, so that order reflects how popular those repositories are rather than any review of ipSAE against them. Open each page to compare what they document and how they install.