Sequence and structure alignments in post-AlphaFold era

Sandun Rajapaksa, Arun S. Konagurthu, Arthur M. Lesk

Research output: Contribution to journalReview articlepeer-review


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.

Original languageEnglish (US)
Article number102539
JournalCurrent Opinion in Structural Biology
StatePublished - Apr 2023

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology


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