Dear reader,

We’re pleased to share an early release of our Mindtrek 2025 conference paper, available exclusively to Foundational members ahead of its official presentation in October. The paper reports on the first systematic accessibility audit of widely used molecular design tools — AlphaFold 3, ColabFold, ESMFold, and PyMOL — evaluated under the EU Accessibility Act (EN 301 549 / WCAG 2.1) using both sighted and screen-reader testing.

For students, the paper demonstrates how accessibility testing can be framed as a rigorous research contribution in the context of biodesign and protein engineering. For educators, it offers a structured, repeatable methodology that can be integrated into coursework, linking Human–Computer Interaction, accessibility, and molecular design practice. More broadly, the study highlights how inclusive design principles apply to the very tools that underpin biodesign education and research.

Read the Preprint (Foundational Access Only).

Best wishes,

Raphael, Biodesign Academy

What Our Accessibility Audit Reveals About Molecular Design Tools

Introduction

This early-release paper from Mindtrek 2025 presents the first systematic accessibility audit of major molecular design tools — AlphaFold 3, ColabFold, ESMFold, and PyMOL. The evaluation applies the EU Accessibility Act (EN 301 549 / WCAG 2.1), using both sighted testing and screen-reader-based assessment.

The research demonstrates how accessibility evaluation can serve as a rigorous scientific contribution in the fields of biodesign and protein engineering.

Why Accessibility in Molecular Design Tools Matters

• Molecular design platforms are central to biodesign education and research.

• If these tools are inaccessible, students, researchers, and educators with disabilities face barriers to participation.

• Inclusive design is not optional; it is a requirement under EU law and a cornerstone of ethical scientific practice.

Key Findings from the Accessibility Audit

1. AlphaFold 3

   • Strengths: High accuracy in structural predictions.

   • Limitations: Inconsistent keyboard navigation and missing alt text in visual outputs.

2. ColabFold

   • Strengths: Integration with Google Colab enables wide access.

   • Limitations: Screen-reader compatibility issues with dynamic rendering.

3. ESMFold

   • Strengths: Efficient computation of large-scale protein structures.

   • Limitations: Poor semantic labeling of interface elements for assistive technologies.

4. PyMOL

   • Strengths: Widely adopted visualization environment.

   • Limitations: Heavy reliance on mouse-based input, with limited alternative interaction models.

Educational and Research Implications

• For Students: Demonstrates how to frame accessibility testing as formal research, bridging biodesign, HCI, and inclusive design.

• For Educators: Provides a structured, repeatable methodology that can be integrated into coursework.

• For Researchers: Highlights gaps where inclusive design principles must be embedded into next-generation computational biology tools.

Broader Impact

• This study represents a first-of-its-kind accessibility evaluation of widely used molecular design tools.

• It reinforces the principle that accessibility is integral to scientific infrastructure, not an afterthought.

• The findings support the ongoing convergence of computational biology, accessibility standards, and biodesign education.

FAQs

Q1. Why was the EU Accessibility Act used as the framework?
The EU Accessibility Act (EN 301 549 / WCAG 2.1) provides legally recognized, rigorous criteria for accessibility compliance across digital tools, making it suitable for international research contexts.

Q2. How does this study contribute to biodesign education?
It provides a methodology students can replicate, connecting accessibility evaluation to protein engineering and computational design coursework.

Q3. What are the next steps for improving accessibility?

• Collaboration with tool developers to address identified issues.

• Expanding audits to additional molecular design platforms.

• Establishing accessibility as a core benchmark in computational biology research.

Summary

The Mindtrek 2025 paper establishes accessibility auditing as a research frontier in molecular design, demonstrating its relevance to students, educators, and biodesign researchers. By assessing AlphaFold 3, ColabFold, ESMFold, and PyMOL, the study shows how inclusive design principles must shape the future of computational biology tools.

👉 Read the Preprint (Foundational Access Only)