The LIG_MAPK_1, or D-site, pattern has two functional regions: a string with two or three basic residues and a chain of alternating hydrophobic residues [12].
STRING: Functional Protein Association Networks.
The gene ontology software STRING (functional protein association networks) was used to analyze protein interactions (https://string-db.org/).
functional" dataType="xsd:string...
To gain an overview of the biological interaction among the identified proteins, we also constructed the protein-protein functional networks using String database.
The ExPASy Proteomics Server [ 10], GoMiner [ 11], DAVID Bioinformatics Resources [ 12, 13], STRING functional protein association networks 8.3 [ 14] and the GeneCards [ 15] bioinformatics tools were used for the functional interpretation of the data.
Predicted H37Rv interologs derived from non- M. tuberculosis experimental PPIs are much more similar to the H37Rv STRING functional associations dataset (with score ≥ 770) than the H37Rv B2H PPI dataset.
Similar improvements are seen for capDSD with unweighted majority vote and functional flow on STRING, though these are not the best performing methods overall, while performance of multi-way cut degrades with augmented pathways.
The functional links in STRING were determined on the basis of Neighbourhood in the Genome, Gene Fusions, Co-occurrence Across Genomes, Co-Expression, Experimental/Biochemical Data, Association in Curated Databases, and Co-Mentioned in PubMed Abstracts [ 13].
Using CellFateScout together with expression data taken from the Connectivity Map project, small molecule targets from STITCH and functional networks from STRING, we performed a systematic search for active pathways triggered by small molecules and stored them in a Small Molecule Mechanisms Database as illustrated in Figure 1B.
