EMERALD-UI: An interactive web application to unveil novel protein biology hidden in the suboptimal-alignment space

TL;DR

EMERALD-UI is an interactive web tool that visualizes stable protein conformations within suboptimal alignment spaces, uncovering hidden biological insights beyond traditional optimal alignments.

Contribution

It introduces a novel web application that explores suboptimal protein alignments to reveal hidden structural and functional biological information.

Findings

Revealed new protein regions and conformations in suboptimal alignments.

Enhanced understanding of protein evolution and function.

Provided an accessible tool for biological discovery.

Abstract

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.