1-20 of 9146
Journal Article
PASS2: update of database of structure-based sequence alignments Open Access
Database, Volume 2025, 2025, baaf072, https://doi.org/10.1093/database/baaf072
Published: 13 November 2025
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SCOPe class distribution of single-member superfamilies and multi-member su... Open Access
Published: 13 November 2025
Figure 2.
SCOPe class distribution of single-member superfamilies and multi-member superfamilies in PASS2.8. The all alpha ( ) class is the most represented class in single-member superfamilies, and the alpha and beta ( ) protein class is the most represented class in multi-member superfamilies.
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Workflow followed in PASS2.8. Superfamily alignments that do not meet the a... Open Access
Published: 13 November 2025
Figure 1.
Workflow followed in PASS2.8. Superfamily alignments that do not meet the alignment assessment criteria undergo clustering of domains. The results of the clustering lead to ‘split superfamilies’, which are independently passed through the pipeline again. Domains identified as outliers with no parent
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Plot representing the changes in the average gap percentage of the problema... Open Access
Published: 13 November 2025
Figure 3.
Plot representing the changes in the average gap percentage of the problematic cases presented by superfamilies. The superfamilies shown here are representative cases, and the full details are provided in Supplementary Table S1 . The x-axis comprises superfamilies arranged by SCOPe class. The SCOPe
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Detailed studies of four problematic superfamilies requiring re-alignment w... Open Access
Published: 13 November 2025
Figure 4.
Detailed studies of four problematic superfamilies requiring re-alignment with the PASS2 protocol. (a) The CoA-dependent acyl transferases superfamily (i) contains four families and automatically matched domains without family annotations, termed as ‘automated matches’. (ii) The k-means clustering a
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Data statistics for cell organelles. ‘Not reported’ sub-cellular location, ... Open Access
Published: 31 October 2025
Figure 4.
Data statistics for cell organelles. ‘Not reported’ sub-cellular location, termed here as a separate category is not shown.
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Distribution of enzyme classes in this database. Numbers of entries in each... Open Access
Published: 31 October 2025
Figure 7.
Distribution of enzyme classes in this database. Numbers of entries in each category are shown. The reactions catalysed by the respective enzyme classes are shown on the right-hand side.
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Database example output against the query—UniProt ID: ‘P00445’; returned in... Open Access
Published: 31 October 2025
Figure 11.
Database example output against the query—UniProt ID: ‘P00445’; returned in a tabular format (upper panel). Cytoscape-generated interactome image (lower panel).
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InTxDB database home page and statistics of datasets. Open Access
Published: 31 October 2025
Figure 2.
InTxDB database home page and statistics of datasets.
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LCDD interface—search results. Open Access
Published: 31 October 2025
Figure 4.
LCDD interface—search results.
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The statistics of using liposomal carriers for (A) therapeutic, (B) diagnos... Open Access
Published: 31 October 2025
Figure 7.
The statistics of using liposomal carriers for (A) therapeutic, (B) diagnostic, and (C) theranostic applications (NR denotes ‘not reported’).
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The statistics of the most frequently used cargoes based on their types, in... Open Access
Published: 31 October 2025
Figure 8.
The statistics of the most frequently used cargoes based on their types, including (A) chemical compounds, (B) lipid compounds, (C) nanoparticles, (D) nucleic acids, and (E) proteins and peptides.
Journal Article
InTxDB: interaction data between gram-negative bacteria secreted effectors and host proteins Open Access
Database, Volume 2025, 2025, baaf070, https://doi.org/10.1093/database/baaf070
Published: 31 October 2025
Journal Article
Liposomal Cancer Drug Database (LCDD): a comprehensive resource for liposome research in cancer therapy and diagnosis Open Access
Database, Volume 2025, 2025, baaf042, https://doi.org/10.1093/database/baaf042
Published: 31 October 2025
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Schematic diagram of Cys-PTMs involved in ROS-related activities: ROS scave... Open Access
Published: 31 October 2025
Figure 1.
Schematic diagram of Cys-PTMs involved in ROS-related activities: ROS scavenging (—|) and ROS producing (→).
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Heatmap of four different ROS-related categories in taxonomic groups based ... Open Access
Published: 31 October 2025
Figure 6.
Heatmap of four different ROS-related categories in taxonomic groups based on domain [ 84 , 85 ].
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Distribution of disease categories (based on disease anatomy) in this datab... Open Access
Published: 31 October 2025
Figure 8.
Distribution of disease categories (based on disease anatomy) in this database. Numbers of entries in each category are shown.
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Tools of InTxDB. (A) Diamond tool: Provides sequence alignment capabilities... Open Access
Published: 31 October 2025
Figure 5.
Tools of InTxDB. (A) Diamond tool: Provides sequence alignment capabilities with customizable parameters, allowing users to analyse and download alignment results. (B) HPInet Prediction tool: Predicts bacterial effector–host interactions based on sequence data or predefined PPI lists, generating net
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LCDD interface—advanced search. Open Access
Published: 31 October 2025
Figure 3.
LCDD interface—advanced search.
Journal Article
ROSBASE1.0: a comprehensive database of reactive oxygen species (ROS): categorization of cell organelles, proteins, taxonomy, and diseases based on ROS-related activities Open Access
Database, Volume 2025, 2025, baaf069, https://doi.org/10.1093/database/baaf069
Published: 31 October 2025
