15+ years of evolution in peptide visualization, from a PhD project to a tool used in over 500 scientific publications
Hi, I'm Dr. Thomas Freeman, the creator of PepDraw and founder of its parent company, Bearing Forward, LLC. In 2009, while working on a biochemistry PhD in the Wimley lab at Tulane University, I had an idea: create a peptide calculator that would look like a typical calculator interface, except the number buttons would be letters matching amino acids. The calculator would compute physicochemical properties including mass, pI, molar extinction coefficient, and net charge at neutral pH.
The first version was built as a Windows executable using Delphi Turbo. But I wanted more—I wanted to quickly render the chemical structure of peptides. The technical limitations meant learning new languages, and thus began a journey through Java, HTML, JavaScript, and PHP to bring the vision to life.
The first Java-based version that could draw peptide structures by stitching together static images. A breakthrough moment that made visualization possible.
Web-based version built with HTML, JavaScript, and PHP. Made peptide visualization accessible to researchers worldwide through their browsers.
Major upgrade with high-quality amino acid drawings, stereochemistry display, non-canonical amino acids, and terminus modifications. This version served the research community faithfully for a decade.
When the host server updated its PHP library in June 2025, deprecated code broke PepDraw 3.0. Rather than a simple fix, this became an opportunity to reimagine what PepDraw could be.
A complete rebuild using Python with AI-assisted development. No longer reliant on static images, PepDraw 4.0 features a robust dynamic rendering engine that generates chemical structures in real-time.
The vision was ambitious: create a dynamic rendering engine that could visualize peptide structures without relying on pre-drawn images. This would unlock countless visualization possibilities unavailable in previous versions.
Using AI as a coding partner, I tackled several major challenges—including the tricky ring geometry of proline. Months of development resulted in a robust modular rendering engine that exceeded my expectations. Everything about the structural visualizations in PepDraw 4.0 is far above and beyond anything ever possible in previous versions. This represents an extraordinary step forward in PepDraw's evolution.
PepDraw will continue to evolve into the premium peptide research and education platform of the future. I hope you enjoy using it as much as I've enjoyed building it and I would love to hear your feedback or answer any questions as you explore PepDraw 4.0.
"Everything about the structural visualizations in PepDraw 4.0 is far above and beyond anything ever possible in previous versions. This represents an extraordinary step forward in PepDraw's evolution."
Experience the next generation of peptide visualization tools
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