ReviewProtein science : a publication of the Protein Society2020
Substitution scoring matrices for proteins - An overview.
Review in Protein science : a publication of the Protein Society, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 44 citations in OpenAlex.
- A deep learning-based score to evaluate multiple sequence alignments.Molecular biology and evolution · 2026Article
- CB-Search: a method for searching for similar protein motifs with biased compositions.BMC bioinformatics · 2026Article
- Exploring the protein universe with distant similarity detection methods.Protein science : a publication of the Protein Society · 2026Review
- MutAnt: mutation annotation tool predicts deleteriousness of missense mutations and improves mutation calling from transcriptomics.Human genetics · 2025Article
- Comparative assessment of physiochemical metrics for the clustering of adaptive immune receptor repertoires.Nucleic acids research · 2025Article
- MFE-ACVP: anti-coronavirus peptide prediction based on multimodal feature extraction and ensemble learning.Briefings in bioinformatics · 2025Article
- Co-evolution of alpha-helical transmembrane protein residues: large-scale variant profiling and complete mutational landscape of 2277 known PDB entries representing 504 unique human protein sequences.Journal of molecular evolution · 2025Article
- Protein Structural Phylogenetics.Genome biology and evolution · 2025Review
- DensePPI-2: a bio-inspired update for sequence-based PPI prediction leveraging mutation rates.Briefings in bioinformatics · 2025Article
- Empirical substitution models of protein evolution: database, relationships, and modeling considerations.Database : the journal of biological databases and curation · 2025Article
- Development of the TSR-based computational method to investigate spike and monoclonal antibody interactions.Frontiers in chemistry · 2025Article
- Article
- tcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs.Briefings in bioinformatics · 2024Article
- Differential amino acid usage leads to ubiquitous edge effect in proteomes across domains of life that can be explained by amino acid secondary structure propensities.Scientific reports · 2024Article
- DeepPI: Alignment-Free Analysis of Flexible Length Proteins Based on Deep Learning and Image Generator.Interdisciplinary sciences, computational life sciences · 2024Article
- Labeling of methyl groups: a streamlined protocol and guidance for the selection ofJournal of biomolecular NMR · 2024Article
- Variations of VEGFR2 Chemical Space: Stimulator and Inhibitory Peptides.International journal of molecular sciences · 2024Article
- Creation of the HIV-1 antisense geneMicrobiology spectrum · 2024Article
- DeepAFP: An effective computational framework for identifying antifungal peptides based on deep learning.Protein science : a publication of the Protein Society · 2023Article
- Proteome-Wide Structural Computations Provide Insights into Empirical Amino Acid Substitution Matrices.International journal of molecular sciences · 2023Article
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2 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Sequence analysis is the primary and simplest approach to discover structural, functional and evolutionary details of related proteins. All the alignment based approaches of sequence analysis make use of amino acid substitution matrices, and the accuracy of the results largely depends on the type of scoring matrices used to perform alignment tasks. An amino acid substitution matrix is a 20 × 20 matrix in which the individual elements encapsulate the rates at which each of the 20 amino acid residues in proteins are substituted by other amino acid residues over time. In contrast to most globular/ordered proteins whose amino acids composition is considered as standard, there are several classes of proteins (e.g., transmembrane proteins) in which certain types of amino acid (e.g., hydrophobic residues) are enriched. These compositional differences among various classes of proteins are manifested in their underlying residue substitution frequencies. Therefore, each of the compositionally distinct class of proteins or protein segments should be studied using specific scoring matrices that reflect their distinct residue substitution pattern. In this review, we describe the development and application of various substitution scoring matrices peculiar to proteins with standard and biased compositions. Along with most commonly used standard matrices (PAM, BLOSUM, MD and VTML) that act as default parameters in various homologs search and alignment tools, different substitution scoring matrices specific to compositionally distinct class of proteins are discussed in detail.
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