ArticleScientific reports2019
Amino acid substitution scoring matrices specific to intrinsically disordered regions in proteins.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
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- PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions.Protein science : a publication of the Protein Society · 2025Article
- tcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs.Briefings in bioinformatics · 2024Article
- SHARK enables sensitive detection of evolutionary homologs and functional analogs in unalignable and disordered sequences.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Sex chromosome-encoded protein homologs: current progress and open questions.Nature structural & molecular biology · 2024Review
- PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions.bioRxiv : the preprint server for biology · 2024Article
- Engineering G protein-coupled receptors for stabilization.Protein science : a publication of the Protein Society · 2024Article
- The Evolution of Temperature and Desiccation-Related Protein Families in Tardigrada Reveals a Complex Acquisition of Extremotolerance.Genome biology and evolution · 2024Article
- CapsNet-MHC predicts peptide-MHC class I binding based on capsule neural networks.Communications biology · 2023Article
- New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions.Frontiers in bioinformatics · 2023Article
- Intrinsically Disordered Proteins: An Overview.International journal of molecular sciences · 2022Review
- Insights from analyses of low complexity regions with canonical methods for protein sequence comparison.Briefings in bioinformatics · 2022Article
- In Silico Studies Reveal Peramivir and Zanamivir as an Optimal Drug Treatment Even If H7N9 Avian Type Influenza Virus Acquires Further Resistance.Molecules (Basel, Switzerland) · 2022Article
- IDPConformerGenerator: A Flexible Software Suite for Sampling the Conformational Space of Disordered Protein States.The journal of physical chemistry. A · 2022Article
- Article
- A Novel Core Effector Vp1 Promotes Fungal Colonization and Virulence ofJournal of fungi (Basel, Switzerland) · 2021Article
- Substitution scoring matrices for proteins - An overview.Protein science : a publication of the Protein Society · 2020Review
- New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release.Evolutionary bioinformatics online · 2020Article
- Suppression of aggregate and amyloid formation by a novel intrinsically disordered region in metazoan Hsp110 chaperones.The Journal of biological chemistryArticle
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
An amino acid substitution scoring matrix encapsulates the rates at which various amino acid residues in proteins are substituted by other amino acid residues, over time. Database search methods make use of substitution scoring matrices to identify sequences with homologous relationships. However, widely used substitution scoring matrices, such as BLOSUM series, have been developed using aligned blocks that are mostly devoid of disordered regions in proteins. Hence, these substitution-scoring matrices are mostly inappropriate for homology searches involving proteins enriched with disordered regions as the disordered regions have distinct amino acid compositional bias, and therefore expected to have undergone amino acid substitutions that are distinct from those in the ordered regions. We, therefore, developed a novel series of substitution scoring matrices referred to as EDSSMat by exclusively considering the substitution frequencies of amino acids in the disordered regions of the eukaryotic proteins. The newly developed matrices were tested for their ability to detect homologs of proteins enriched with disordered regions by means of SSEARCH tool. The results unequivocally demonstrate that EDSSMat matrices detect more number of homologs than the widely used BLOSUM, PAM and other standard matrices, indicating their utility value for homology searches of intrinsically disordered proteins.
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