ArticleNucleic acids research2011
Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Two D-loop resolution systems enable natural genetic transformation in bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A nuclease domain fused to the Snf2 helicase confers antiphage defence in coral-associated Halomonas meridiana.Microbial biotechnology · 2024Article
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- Crystal structure and initial characterization of a novel archaeal-like Holliday junction-resolving enzyme from Thermus thermophilus phage Tth15-6.Acta crystallographica. Section D, Structural biology · 2022Article
- The key players of parthanatos: opportunities for targeting multiple levels in the therapy of parthanatos-based pathogenesis.Cellular and molecular life sciences : CMLS · 2022Review
- Genomic discovery and structural dissection of a novel type of polymorphic toxin system in gram-positive bacteria.Computational and structural biotechnology journal · 2022Article
- Structure-Based Deep Mining Reveals First-Time Annotations for 46 Percent of the Dark Annotation Space of the 9,671-Member Superproteome of the Nucleocytoplasmic Large DNA Viruses.Journal of virology · 2020Article
- Type II Restriction-Modification System fromPathogens (Basel, Switzerland) · 2020Article
- A complex comprising C15ORF41 and Codanin-1: the products of two genes mutated in congenital dyserythropoietic anaemia type I (CDA-I).The Biochemical journal · 2020Article
- The pathogenesis, diagnosis and management of congenital dyserythropoietic anaemia type I.British journal of haematology · 2019Review
- Article
- Site specific target binding controls RNA cleavage efficiency by the Kaposi's sarcoma-associated herpesvirus endonuclease SOX.Nucleic acids research · 2018Article
- Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer.Journal of bacteriology · 2017Article
- Mitochondrial Mechanisms of Neuronal Cell Death: Potential Therapeutics.Annual review of pharmacology and toxicology · 2017Review
- A nuclease that mediates cell death induced by DNA damage and poly(ADP-ribose) polymerase-1.Science (New York, N.Y.) · 2016Article
- Genomic survey and expression analysis of DNA repair genes in the genus Leptospira.Molecular genetics and genomics : MGG · 2016Article
- Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006.Frontiers in microbiology · 2015Article
- Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix.Nucleic acids research · 2014Article
- Type II restriction endonucleases--a historical perspective and more.Nucleic acids research · 2014Review
- Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA.Nucleic acids research · 2014Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
PD-(D/E)XK nucleases, initially represented by only Type II restriction enzymes, now comprise a large and extremely diverse superfamily of proteins. They participate in many different nucleic acids transactions including DNA degradation, recombination, repair and RNA processing. Different PD-(D/E)XK families, although sharing a structurally conserved core, typically display little or no detectable sequence similarity except for the active site motifs. This makes the identification of new superfamily members using standard homology search techniques challenging. To tackle this problem, we developed a method for the detection of PD-(D/E)XK families based on the binary classification of profile-profile alignments using support vector machines (SVMs). Using a number of both superfamily-specific and general features, SVMs were trained to identify true positive alignments of PD-(D/E)XK representatives. With this method we identified several PFAM families of uncharacterized proteins as putative new members of the PD-(D/E)XK superfamily. In addition, we assigned several unclassified restriction enzymes to the PD-(D/E)XK type. Results show that the new method is able to make confident assignments even for alignments that have statistically insignificant scores. We also implemented the method as a freely accessible web server at http://www.ibt.lt/bioinformatics/software/pdexk/.
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