Hi, does anyone know what tools or software can be used to create 2D protein topology diagrams like the one below? I’m looking to make figures that show transmembrane domains, loops, and labeling like this — ideally with customizable colors and shapes. Any suggestions would be really helpful. Thanks!
If you're looking to create professional 2D protein topology diagrams – the kind that show transmembrane domains as boxes, loops as squiggly lines, and let you label everything with custom colors – here are your best options in plain English:
For quick and easy solutions, try web tools like Protter or BioRender. Protter is super handy because you just paste a UniProt ID and it automatically generates a clean topology diagram with membrane helices and loops already mapped out. BioRender works like PowerPoint for biologists – they have pre-made protein templates you can drag, drop, and customize with different colors and labels. Both will give you nice-looking figures fast, though you might hit some limits if you need very specific designs.
If you need more control and don't mind some manual work, illustration software is the way to go. Lucidchart or Draw.io (both free) are like digital whiteboards where you can build your diagram from scratch using simple shapes – rectangles for domains, wavy lines for loops, and text boxes for labels. For even more precision, Inkscape is a free alternative to Adobe Illustrator where you can craft every detail exactly how you want it, though there's a learning curve.
If you work with lots of proteins or need to automate things, coding tools might be worth learning. With Python (using Matplotlib) or R (using drawProteins package), you can write scripts to generate diagrams directly from protein data files. This is powerful if you're making many similar figures, but obviously requires some programming comfort.
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