ArticleGenome biology2007
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Identification and characterization of components of the Candida albicans inner kinetochore.Genetics · 2025Article
- An interpretable alphabet for local protein structure search based on amino acid neighborhoods.Bioinformatics (Oxford, England) · 2025Article
- An integrated structural and biophysical approach to study carbon metabolism inQRB discovery · 2025Review
- Functional genomic analysis of genes important for Candida albicans fitness in diverse environmental conditions.Cell reports · 2024Article
- Allelic variations in the chpG effector gene within Clavibacter michiganensis populations determine pathogen host range.PLoS pathogens · 2024Article
- A novel replication initiation region encoded in a widespread Acinetobacter plasmid lineage carrying a blaNDM-1 gene.PloS one · 2024Article
- Essential amino acids in the Plant-Conserved and Class-Specific Regions of cellulose synthases.Plant physiology · 2023Article
- Promiscuity of response regulators for thioredoxin steers bacterial virulence.Nature communications · 2022Article
- Structural and functional characterization of a putative de novo gene in Drosophila.Nature communications · 2021Article
- Substrate-recognition mechanism of tomato β-galactosidase 4 using X-ray crystallography and docking simulation.Planta · 2020Article
- Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet.Biomolecules · 2020Article
- Ab initio folding of a trefoil-fold motif reveals structural similarity with a β-propeller blade motif.Protein science : a publication of the Protein Society · 2020Article
- PMP-diketopiperazine adducts form at the active site of a PLP dependent enzyme involved in formycin biosynthesis.Chemical communications (Cambridge, England) · 2019Article
- Acetyl-CoA-mediated activation of Mycobacterium tuberculosis isocitrate lyase 2.Nature communications · 2019Article
- ANKRD9 is a metabolically-controlled regulator of IMPDH2 abundance and macro-assembly.The Journal of biological chemistry · 2019Article
- Membrane protein-regulated networks across human cancers.Nature communications · 2019Article
- SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information.PloS one · 2018Article
- Rice Cellulose SynthaseA8 Plant-Conserved Region Is a Coiled-Coil at the Catalytic Core Entrance.Plant physiology · 2017Article
- Enzymatic hydrolysis by transition-metal-dependent nucleophilic aromatic substitution.Nature chemical biology · 2016Article
- Protein flexibility in the light of structural alphabets.Frontiers in molecular biosciences · 2015Review
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a novel protein structure database search tool, 3D-BLAST, that is useful for analyzing novel structures and can return a ranked list of alignments. This tool has the features of BLAST (for example, robust statistical basis, and effective and reliable search capabilities) and employs a kappa-alpha (kappa, alpha) plot derived structural alphabet and a new substitution matrix. 3D-BLAST searches more than 12,000 protein structures in 1.2 s and yields good results in zones with low sequence similarity.
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