1-20 of 9146
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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
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.
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
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Flowchart of ROSBase curation. Open Access
Published: 31 October 2025
Figure 2.
Flowchart of ROSBase curation.
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Workflow (integrating backend and frontend) of ROSBase1.0 webserver. Open Access
Published: 31 October 2025
Figure 3.
Workflow (integrating backend and frontend) of ROSBase1.0 webserver.
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The taxonomic classification of the database. Numbers of entries in each ca... Open Access
Published: 31 October 2025
Figure 5.
The taxonomic classification of the database. Numbers of entries in each category are shown.
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(a) Disease categories per protein entry (UniProt ID). (b) Pie chart repres... Open Access
Published: 31 October 2025
Figure 9.
(a) Disease categories per protein entry (UniProt ID). (b) Pie chart representation of each disease category and corresponding UniProt IDs.
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Interactome around Tp53, (a) derived from the STRING network and (b) regula... Open Access
Published: 31 October 2025
Figure 10.
Interactome around Tp53, (a) derived from the STRING network and (b) regulatory pathways of Tp53; inhibition (—|) and interaction (→).
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The workflow of InTxDB. The construction of InTxDB involves three main stag... Open Access
Published: 31 October 2025
Figure 1.
The workflow of InTxDB. The construction of InTxDB involves three main stages: data collection, data processing, and web construction. Data collection integrates three components: TxSE-human PPIs from databases and literature, structural data from PDB and AlphaFold DB, and interaction networks deriv
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Two modules of InTxDB. (A) Browse module: Users can filter interaction data... Open Access
Published: 31 October 2025
Figure 3.
Two modules of InTxDB. (A) Browse module: Users can filter interaction data using options such as bacterial species, secretion system type, and protein length to quickly locate relevant information. (B) Detailed information page: Displays comprehensive details on selected interactions, including pro
