Sequence and structure alignments in post-AlphaFold era |
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| Affiliation: | 1. Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA;2. Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA;3. Howard Hughes Medical Institute, Chevy Chase, MD, USA;4. Department of Biological and Chemical Engineering, Dongyang Mirae University, Seoul, South Korea;5. Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark;6. Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA;7. Ikerbasque, Basque Foundation for Science and Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain;8. Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA |
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| 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. |
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| Keywords: | Protein evolution Amino-acid sequence alignment Structure alignment Structure prediction |
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