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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
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 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 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
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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
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
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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
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(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
RRMScorer: A web server for predicting RNA recognition motif binding preferences
Nucleic Acids Research, gkaf367, https://doi.org/10.1093/nar/gkaf367
Published: 07 May 2025
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Graphical Abstract
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Nucleic Acids Research
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The UniProt website API: facilitating programmatic access to protein knowledge
Published: 07 May 2025
Graphical Abstract
Graphical Abstract
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UniProt website API service architecture: This high-level architecture diag...
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Nucleic Acids Research
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The UniProt website API: facilitating programmatic access to protein knowledge
Published: 07 May 2025
Figure 1.
UniProt website API service architecture: This high-level architecture diagram shows a system where different clients (web, mobile, and programmatic) interact with back-end services via an API Gateway. ( a ) The API Gateway routes requests to ( b ) multiple REST services (UniProtKB, UniRef, UniParc,
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Genome (A and B) and taxonomic binning results (C) from the CAMI Benchmarki...
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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
Figure 2.
Genome (A and B) and taxonomic binning results (C) from the CAMI Benchmarking Portal for the CAMI II marine dataset. ( A ) Number of genomes recovered with <10% contamination and >50%, >70%, and >90% completeness, denoting low- to high-quality recovered genomes. ( B ) Scatter plot of ave
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Taxonomic profiling results from the CAMI Benchmarking Portal for the CAMI ...
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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
Figure 3.
Taxonomic profiling results from the CAMI Benchmarking Portal for the CAMI II marine dataset at the genus level. The left panel shows purity ( x -axis) versus completeness ( y -axis), while the right panel shows 2 − L1 norm ( x -axis) versus 16 − weighted UniFrac ( y -axis). Values are averages acro
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Graphical Abstract
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Nucleic Acids Research
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Web-based GTalign: bridging speed and accuracy in protein structure analysis
Published: 07 May 2025
Graphical Abstract
Graphical Abstract
Journal Article
The structure of the Vibrio natriegens 70S ribosome in complex with the proline-rich antimicrobial peptide Bac5(1–17)
Nucleic Acids Research, Volume 53, Issue 8, 8 May 2025, gkaf324, https://doi.org/10.1093/nar/gkaf324
Published: 07 May 2025
