ArticleProteins2021
New amino acid substitution matrix brings sequence alignments into agreement with structure matches.
Article in Proteins, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 27 citations in OpenAlex.
- The sequence alignment problem: boundary conditions as the unifying principle.Briefings in bioinformatics · 2026Review
- Much ado about nothing: modeling amino acid replacement with predicted protein structures.Bioinformatics (Oxford, England) · 2026Article
- MODEL-FREE INFERENCE FOR CHARACTERIZING PROTEIN MUTATIONS THROUGH A COEVOLUTIONARY LENS.The annals of applied statistics · 2026Article
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- Major advances in protein function assignment by remote homolog detection with protein language models - A review.Current opinion in structural biology · 2025Review
- Improving the Annotations of JCVI-Syn3a Proteins.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The Historical Evolution and Significance of Multiple Sequence Alignment in Molecular Structure and Function Prediction.Biomolecules · 2024Review
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- GradPose: a very fast and memory-efficient gradient descent-based tool for superimposing millions of protein structures from computational simulations.Bioinformatics (Oxford, England) · 2023Article
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- Improved global protein homolog detection with major gains in function identification.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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- New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions.Frontiers in bioinformatics · 2023Article
- JSONWP: a static website generator for protein bioinformatics research.Bioinformatics advances · 2023Article
- Fast and accurate Ab Initio Protein structure prediction using deep learning potentials.PLoS computational biology · 2022Article
- New substitutions on NS1 protein from influenza A (H1N1) virus: Bioinformatics analyses of Indian strains isolated from 2009 to 2020.Health science reports · 2022Article
- Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Protein sequence matching presently fails to identify many structures that are highly similar, even when they are known to have the same function. The high packing densities in globular proteins lead to interdependent substitutions, which have not previously been considered for amino acid similarities. At present, sequence matching compares sequences based only upon the similarities of single amino acids, ignoring the fact that in densely packed protein, there are additional conservative substitutions representing exchanges between two interacting amino acids, such as a small-large pair changing to a large-small pair substitutions that are not individually so conservative. Here we show that including information for such pairs of substitutions yields improved sequence matches, and that these yield significant gains in the agreements between sequence alignments and structure matches of the same protein pair. The result shows sequence segments matched where structure segments are aligned. There are gains for all 2002 collected cases where the sequence alignments that were not previously congruent with the structure matches. Our results also demonstrate a significant gain in detecting homology for "twilight zone" protein sequences. The amino acid substitution metrics derived have many other potential applications, for annotations, protein design, mutagenesis design, and empirical potential derivation.
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