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Frequency distribution of superfamilies with respect to true positive rates... Open Access
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
Image
The glycolysis pathway. Enzymes are represented by light blue boxes; yellow... Open Access
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
Journal Article
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database Open Access
Sarthak Joshi and others
Database, Volume 2025, 2025, baaf035, https://doi.org/10.1093/database/baaf035
Published: 09 May 2025
Image
GenDiS3 workflow for search and validation of homologs. Open Access
Published: 09 May 2025
Figure 1.
GenDiS3 workflow for search and validation of homologs.
Image
The GenDiS3 web interface for visualizing taxonomic distribution and DAs. (... Open Access
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.
Image
Mutations found in LOG genes from the Solanum genus mapped on CRMP... Open Access
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
Image
(a) Barplot displaying average Gini coefficient (0–1) from 2013 to 2022. Ea... Open Access
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
Image
Gini coefficient (0–1) of the number of FPEs of human proteins. Open Access
Published: 07 May 2025
Figure 3.
Gini coefficient (0–1) of the number of FPEs of human proteins.
Image
Information content and number of FPEs (in log scale) of proteins in 2022. ... Open Access
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
Image
Boxplots showing Spearman’s coefficient between the number of FPEs and the ... Open Access
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
Image
The figure shows the diversity and distribution of anticancer peptides. Open Access
Published: 07 May 2025
Figure 2.
The figure shows the diversity and distribution of anticancer peptides.
Journal Article
CancerPPD2: an updated repository of anticancer peptides and proteins Open Access
Milind Chauhan and others
Database, Volume 2025, 2025, baaf030, https://doi.org/10.1093/database/baaf030
Published: 07 May 2025
Image
Information content of proteins studied experimentally from 2013 to 2022 in... Open Access
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
Image
(a) Barplot of the number of years between annotation and publication for e... Open Access
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
Image
The figure shows the complete architecture of the database. Open Access
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 Open Access
An Phan and others
Database, Volume 2025, 2025, baaf036, https://doi.org/10.1093/database/baaf036
Published: 07 May 2025
Image
The whole map of the the network of neurological diseases related cell sign... Open Access
Published: 02 May 2025
Figure 4.
The whole map of the the network of neurological diseases related cell signaling transduction pathways, and figures of heatmap generated from disease data collected from DiSignAtlas website and the PPI network of TUBA4A from NDAtlas website.
Journal Article
STCDB4ND: a signal transduction classification database for neurological diseases Open Access
Boyan Gong and others
Database, Volume 2025, 2025, baaf032, https://doi.org/10.1093/database/baaf032
Published: 02 May 2025
Image
The flowchart of the key factor recognition algorithm, in which M is the tr... Open Access
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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