ArticleProceedings of the National Academy of Sciences of the United States of America2005
Solving the protein sequence metric problem.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 223 papers.
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Who cites it
223 citing papers in PubMed, 469 citations in OpenAlex.
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- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- Deciphering small sequence differences in T cell receptor-antigen pairing.Nature communications · 2026Article
- BenchRep-T: A Systematic Evaluation of T-Cell Repertoire-Based Disease Diagnostics.bioRxiv : the preprint server for biology · 2026Article
- A multi-ethnic reference map of T cell receptor germline diversity reveals evidence of natural selection on alpha chain genes.Nature communications · 2026Article
- Immunodominance Hierarchy of Endogenous BBN963 Bladder Cancer Antigens Remains Stable Under Anti-PD1 and Anti-CTLA4 Immunotherapy.bioRxiv : the preprint server for biology · 2026Article
- Predicting protein-nucleic acid interactions via protein language models with biophysical and evolutionary priors.iScience · 2026Article
- CAPHEINE, or everything and the kitchen sink: a workflow for automating selection analyses using HyPhy.bioRxiv : the preprint server for biology · 2026Article
- Evaluating the utility of amino acid similarity-aware kmers to represent TCR repertoires for classification.PLoS computational biology · 2026Article
- DEX: a consensus-based amino acid exchangeability measure for improved codon substitution modelling.bioRxiv : the preprint server for biology · 2026Article
- Characterizing Physicochemical Selection in Protein Evolution with Property-Informed Models (PRIME).bioRxiv : the preprint server for biology · 2026Article
- Resurrected nitrogenases recapitulate canonical N-isotope biosignatures over two billion years.Nature communications · 2026Article
- TCRLens: structure-aware equivariant graph learning for TCR-pMHC-I recognition and immunogenic epitope discovery.Bioinformatics advances · 2026Article
- Article
- Comparative assessment of physiochemical metrics for the clustering of adaptive immune receptor repertoires.Nucleic acids research · 2025Article
163 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Biological sequences are composed of long strings of alphabetic letters rather than arrays of numerical values. Lack of a natural underlying metric for comparing such alphabetic data significantly inhibits sophisticated statistical analyses of sequences, modeling structural and functional aspects of proteins, and related problems. Herein, we use multivariate statistical analyses on almost 500 amino acid attributes to produce a small set of highly interpretable numeric patterns of amino acid variability. These high-dimensional attribute data are summarized by five multidimensional patterns of attribute covariation that reflect polarity, secondary structure, molecular volume, codon diversity, and electrostatic charge. Numerical scores for each amino acid then transform amino acid sequences for statistical analyses. Relationships between transformed data and amino acid substitution matrices show significant associations for polarity and codon diversity scores. Transformed alphabetic data are used in analysis of variance and discriminant analysis to study DNA binding in the basic helix-loop-helix proteins. The transformed scores offer a general solution for analyzing a wide variety of sequence analysis problems.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.