Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments

Abstract

Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-based approaches. Encoding three-dimensional protein structures using a simplified structure-aware alphabet can lead to compact, comparable strings that retain key spatial relationships. Although this enables comparison, structure-aware alignments can experience misaligned regions, particularly when comparing proteins with substantial divergence in fold architecture. To address this, a web-based resource, StructomeAlignViewer, is introduced in this work for evaluating the quality of structure-aware alignments through both spatial mapping of alignment co..