An Introduction to Sequence Similarity (“Homology”) Searching

By William R. Pearson. Current Protocols in Bioinformatics, 2013

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Engineering a Rugged Nanoscaffold To Enhance Plug-and-Display Vaccination (2018, unknown): “58 In comparison, a similar alignment was done for Δ N1-SpyCatcher which is an N-terminally truncated version of SpyCatcher for reduced immunogenicity.”
Consensus protein design (2016, background): “Unfortunately, MSA methods tend to vary significantly, and there is currently no quantitative measure for the quality of alignment (Nuin et al., 2006; Kemena and Notredame, 2009; Pearson, 2013).”
Single-sequence protein structure prediction using language models from deep learning (2021, background): “…using ML nonetheless remains a challenge: the requirement in AlphaFold2 for co-evolutionary information from MSAs makes it less performative with proteins that lack sequence homologs, currently estimated at ~20% of all metagenomic protein sequences 9 and ~11% of eukaryotic and viral proteins 10 .”