1-20 of 8938
Journal Article
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database
Database, Volume 2025, 2025, baaf035, https://doi.org/10.1093/database/baaf035
Published: 09 May 2025
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GenDiS3 workflow for search and validation of homologs.
Published: 09 May 2025
Figure 1.
GenDiS3 workflow for search and validation of homologs.
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The GenDiS3 web interface for visualizing taxonomic distribution and DAs. (...
Published: 09 May 2025
Figure 3.
The GenDiS3 web interface for visualizing taxonomic distribution and DAs. (a) Sunburst chart (interactive) showing the taxonomic distribution of a superfamily. (b) SCOP DAs of a superfamily.
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Mutations found in LOG genes from the Solanum genus mapped on CRMP...
Published: 09 May 2025
Figure 5.
Mutations found in LOG genes from the Solanum genus mapped on CRMP (LOG8) from A. thaliana (PDB: 1YDH). Red represents location of deletions, yellow represents location of insertions, and green marks the flanking residues for intronic mutations. The orange area marks the inferred substrate bindi
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The glycolysis pathway. Enzymes are represented by light blue boxes; yellow...
Published: 09 May 2025
Figure 4.
The glycolysis pathway. Enzymes are represented by light blue boxes; yellow boxes correspond to intermediate molecules within the pathway. Colourful boxes flanking the pathway represent the DA of each enzyme where each SCOP domain is represented by the superfamily code. SF 53067: c.55.1 (actin-like
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Frequency distribution of superfamilies with respect to true positive rates...
Published: 09 May 2025
Figure 2.
Frequency distribution of superfamilies with respect to true positive rates of the search strategy. The dashed lines indicate the 5th, 15th, 25th, 50th, and 75th percentiles of the data. From the plot, we can observe that 50% of the superfamilies have a true positive rate of >0.77 for DELTA-BLAST
Journal Article
CancerPPD2: an updated repository of anticancer peptides and proteins
Database, Volume 2025, 2025, baaf030, https://doi.org/10.1093/database/baaf030
Published: 07 May 2025
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Information content of proteins studied experimentally from 2013 to 2022 in...
Published: 07 May 2025
Figure 1.
Information content of proteins studied experimentally from 2013 to 2022 in (a) articles describing high-throughput (>100 proteins per article; blue boxes) vs. low-throughput experiments (≤100 proteins per article; orange boxes) and (b) all articles. Each box shows the distribution of information
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(a) Barplot of the number of years between annotation and publication for e...
Published: 07 May 2025
Figure 6.
(a) Barplot of the number of years between annotation and publication for experimental GO annotations of human proteins. The vertical line shows the median of this distribution at 4 years. (b) Barplot of the distribution of publication year and annotation year for GO experimental annotations of huma
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The figure shows the complete architecture of the database.
Published: 07 May 2025
Figure 1.
The figure shows the complete architecture of the database.
Journal Article
A longitudinal analysis of function annotations of the human proteome reveals consistently high biases
Database, Volume 2025, 2025, baaf036, https://doi.org/10.1093/database/baaf036
Published: 07 May 2025
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(a) Barplot displaying average Gini coefficient (0–1) from 2013 to 2022. Ea...
Published: 07 May 2025
Figure 2.
(a) Barplot displaying average Gini coefficient (0–1) from 2013 to 2022. Each bar indicates one of three knowledge metrics of human proteins: term count (dark green), unique term count (light green), and information content (black) in one of three GO aspects. Error bars extend one standard deviation
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Gini coefficient (0–1) of the number of FPEs of human proteins.
Published: 07 May 2025
Figure 3.
Gini coefficient (0–1) of the number of FPEs of human proteins.
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Information content and number of FPEs (in log scale) of proteins in 2022. ...
Published: 07 May 2025
Figure 4.
Information content and number of FPEs (in log scale) of proteins in 2022. Each black dot represents the number of FPEs and the information content per protein within an aspect (MFO, BPO, CCO) in 2022. Highlighted genes (coloured dots) have one data point for each year from 2013 to 2022. Highlighted
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Boxplots showing Spearman’s coefficient between the number of FPEs and the ...
Published: 07 May 2025
Figure 5.
Boxplots showing Spearman’s coefficient between the number of FPEs and the gain in information content (in MFO and BPO) of disease-associated proteins. Triangles (with disease names labelled) indicate diseases with a significant Spearman correlation, and circles indicate diseases without significant
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The figure shows the diversity and distribution of anticancer peptides.
Published: 07 May 2025
Figure 2.
The figure shows the diversity and distribution of anticancer peptides.
Journal Article
STCDB4ND: a signal transduction classification database for neurological diseases
Database, Volume 2025, 2025, baaf032, https://doi.org/10.1093/database/baaf032
Published: 02 May 2025
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The flowchart of the key factor recognition algorithm, in which M is the tr...
Published: 02 May 2025
Figure 1.
The flowchart of the key factor recognition algorithm, in which M is the transition matrix, R refers to the vector of node-ranks, d is damping factor, and ε is the iteration accuracy.
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Schematic diagram of the data processing and database structure of STCDB4ND...
Published: 02 May 2025
Figure 2.
Schematic diagram of the data processing and database structure of STCDB4ND in this study.
