How to See the Hidden Shapes of Proteins express
Proteins are the molecular machines of life. They fold into complex three-dimensional shapes, like a sheet of paper into origami. But if you fold the paper a bit differently, you get a different figure. Likewise, a protein can take on several forms, and that determines how it works.
Usually, scientists compare proteins by their sequences — chains of amino acids. It's like comparing book texts without looking at the illustrations. But now there's a tool called EMERALD-UI. It shows not only the primary shape of a protein but also alternative versions that hide in "suboptimal" alignments.
It's like looking at the night sky not only through the most powerful telescope but also through a side finder scope: sometimes you see things there that the main lens misses. The tool is free and runs right in your browser.
Original abstract
as written by the authors arXiv:2602.12730
Life over the past four billion years has been shaped by proteins and their capacity to assemble into three dimensional conformations. Protein sequence alignments have been the enabling technology for exploring the evolution and functional adaptation of proteins across the tree of life. Recent advancements in scaling the prediction of three dimensional protein structures from primary sequence alone, revealed that different modes of conservation and function operate on the sequence and structure level. This difference in protein conservation patterns and their underlying functional change that could emerge in suboptimal alignment configurations is often ignored in optimal protein alignment approaches. We introduce EMERALD-UI, an open-source interactive web application which is designed to reveal unexplored biology by visualising stable structural conformations or protein regions hidden in the suboptimal alignment space. Availability: EMERALD-UI is available at https://algbio.github.io/emerald-ui/. Contact: hdrost001@dundee.ac.uk or alexandru.tomescu@helsinki.fi.
A protein can have several stable shapes, and switching between them sometimes acts like a molecular switch.