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Journal
Nucleic Acids Research
Publishes the results of leading edge research into physical, chemical, biochemical and biological aspects of nucleic acids and proteins involved in nucleic acid metabolism and/or interactions. Fully open access.
Journal
NAR Cancer
NAR Cancer is an open access journal the publishes research at the intersection
of the nucleic acids research and cancer fields.
Journal
NAR Genomics and Bioinformatics
NAR Genomics and Bioinformatics is an open access journal with an interdisciplinary focus on genomics and bioinformatics large-scale data analysis. It publishes high-quality results, analysis and methods in all aspects of genomics and bioinformatics.
Journal
NAR Molecular Medicine
NAR Molecular Medicine is a cutting-edge new journal in the NAR family portfolio. The journal will be fully open access and will publish original research and critical reviews
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Validating the PARTI workflow in vitro and in cells using E. c...
Published: 08 May 2025
Figure 2.
Validating the PARTI workflow in vitro and in cells using E. coli PheRS and tRNA Phe ( A ) Intact tRNA LC-MS analysis of the products resulting from in vitro acylation of tRNA Phe with Phe and PheRS. The total ion chromatogram (TIC) of the reaction mixture is shown along with the deconvolute
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Controls and an internal standard facilitate comparisons across PARTI sampl...
Published: 08 May 2025
Figure 3.
Controls and an internal standard facilitate comparisons across PARTI samples. ( A ) Shown are overlaid EICs of Leu–Enk (rightmost peak, gray, calc [M + H]: 556.2766 Da) and Phe-Ade (leftmost peaks, green, calc [M + H]: 415.1724 Da). ( B ) Shown is a bar graph comparing raw Phe-Ade peak area sums co
Image
Validating PARTI in vitro and in cells using M. alvi PylR...
Published: 08 May 2025
Figure 4.
Validating PARTI in vitro and in cells using M. alvi PylRS/tRNA Pyl and BocK. ( A ) The secondary structure of M. alvi tRNA Pyl bound to o-Pyl and the structure of BocK. ( B ) In vitro acylation of tRNA Pyl with PylRS and BocK followed by PARTI analysis produces the EICs shown at right. T
Journal Article
Monitoring monomer-specific acyl–tRNA levels in cells with PARTI
Nucleic Acids Research, Volume 53, Issue 8, 8 May 2025, gkaf327, https://doi.org/10.1093/nar/gkaf327
Published: 08 May 2025
Image
3-Prime Adenosine-Retaining aminoacyl–tRNA Isolation (PARTI) reports on mon...
Published: 08 May 2025
Figure 1.
3-Prime Adenosine-Retaining aminoacyl–tRNA Isolation (PARTI) reports on monomer-specific tRNA acylation in cells. ( A ) Schematic showing three states of tRNA—monoacylated, misacylated, or diacylated—that can exist in Escherichia coli expressing an aaRS/tRNA pair and supplemented with substrate. A
Image
(R) - and (S) -β2-hydroxy a...
Published: 08 May 2025
Figure 5.
(R) - and (S) - β 2 -hydroxy acids are not equivalent substrates for PylRS in cells. ( A ) Structures of OH-BocK, ( R) -β 2 -OH-BocK, and ( S) -β 2 -OH-BocK. ( B ) Shown is a bar graph displaying the relative A norm values when 0.1 mM of each monomer in panel (A) is added to E. coli C3
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Benzylmalonate derivatives are substrates for FRSA in cells. ( A ) Structur...
Published: 08 May 2025
Figure 6.
Benzylmalonate derivatives are substrates for FRSA in cells. ( A ) Structures of meta -bromo-phenylalanine ( m -Br-Phe), meta -bromo-2-benzylmalonate ( m -Br-bma), meta -methyl-2-benzylmalonate ( m -CH 3 -bma), and meta -trifluoromethyl- 2-benzylmalonate ( m -CF 3 -bma). ( B ) Structure and calc
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Metabolism of PylRS Substrates in vivo is observable from PARTI wi...
Published: 08 May 2025
Figure 7.
Metabolism of PylRS Substrates in vivo is observable from PARTI with tRNA Pyl . ( A ) Deconvoluted LC-HRMS spectra of sfGFP-200TAG purified from E. coli Top10 cells supplemented with 1 mM BocK (light green, expected mass: 27 662.3 Da) or 1 mM N-Me BocK (dark green, expected mass: 27 676.3 Da). T
Journal Article
The UniProt website API: facilitating programmatic access to protein knowledge
Nucleic Acids Research, gkaf394, https://doi.org/10.1093/nar/gkaf394
Published: 07 May 2025
Journal Article
CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software
Nucleic Acids Research, gkaf369, https://doi.org/10.1093/nar/gkaf369
Published: 07 May 2025
Journal Article
AlphaLasso—a web server to identify loop and lasso motifs in 3D structure of biopolymers
Nucleic Acids Research, gkaf375, https://doi.org/10.1093/nar/gkaf375
Published: 07 May 2025
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Graphical Abstract
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Nucleic Acids Research
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CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software
Published: 07 May 2025
Graphical Abstract
Graphical Abstract
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Assembly results from the CAMI Benchmarking Portal for the CAMI II marine d...
in
Nucleic Acids Research
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CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software
Published: 07 May 2025
Figure 1.
Assembly results from the CAMI Benchmarking Portal for the CAMI II marine dataset. ( A ) Heatmap table of public results. Blue indicates better performance and red indicates worse. Assemblies are assessed with MetaQUAST using the underlying genomes and ranked with a combination of metrics (see main
Image
Graphical Abstract
in
Nucleic Acids Research
>
AlphaLasso—a web server to identify loop and lasso motifs in 3D structure of biopolymers
Published: 07 May 2025
Graphical Abstract
Graphical Abstract
Image
Protein analysis result. At the top of the page is the UniProtKB ID of the ...
in
Nucleic Acids Research
>
AlphaLasso—a web server to identify loop and lasso motifs in 3D structure of biopolymers
Published: 07 May 2025
Figure 3.
Protein analysis result. At the top of the page is the UniProtKB ID of the protein, model number, and protein name. ( A ) Button to alternate between lasso information and protein information. The protein information tab contains the organism and cross-references to other databases. ( B ) Lasso fing
