Sequence and structure alignments in post-AlphaFold era
- PMID: 36753924
- DOI: 10.1016/j.sbi.2023.102539
Sequence and structure alignments in post-AlphaFold era
Abstract
Sequence alignment is fundamental for analyzing protein structure and function. For all but closely-related proteins, alignments based on structures are more accurate than alignments based purely on amino-acid sequences. However, the disparity between the large amount of sequence data and the relative paucity of experimentally-determined structures has precluded the general applicability of structure alignment. Based on the success of AlphaFold (and its likes) in producing high-quality structure predictions, we suggest that when aligning homologous proteins, lacking experimental structures, better results can be obtained by a structural alignment of predicted structures than by an alignment based only on amino-acid sequences. We present a quantitative evaluation, based on pairwise alignments of sequences and structures (both predicted and experimental) to support this hypothesis.
Keywords: Amino-acid sequence alignment; Protein evolution; Structure alignment; Structure prediction.
Copyright © 2023 Elsevier Ltd. All rights reserved.
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