PMC:4331677 / 7914-9161 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4331677","sourcedb":"PMC","sourceid":"4331677","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4331677","text":"We extracted all human targets and ligands from sc-PDB database [16], which is an annotated archive of the druggable binding sites extracted from the Protein Data Bank [17]. In this work, we set the amino acid residues possessing at least one atom within eight angstroms around the ligand as binding sites. A target might possess more than one binding sites, and each binding site might interact with several ligands (Figure 2). After removing the redundance and checking the consistency, we got 836 targets and 2710 corresponding ligands. Among them, 782 single binding site targets interact with 1988 ligands to form 2561 interaction pairs, and other multiple binding sites targets interact with 722 ligands to form 854 interaction pairs. According to a published method [9], for each binding site, we generated as many negative site-ligand pairs as the known positive pairs by combining the site with randomly chosen ligands among the other sites' ligands (excluding those known to interact with the given target). Of course, this protocol may generate false negative data for some ligands could actually interact with the site whereas they have not been experimentally tested. Totally, 6830 site-ligand pairs include in our data set (Table 1).","tracks":[{"project":"2_test","denotations":[{"id":"25707321-21398668-14839511","span":{"begin":65,"end":67},"obj":"21398668"},{"id":"25707321-18676415-14839512","span":{"begin":774,"end":775},"obj":"18676415"}],"attributes":[{"subj":"25707321-21398668-14839511","pred":"source","obj":"2_test"},{"subj":"25707321-18676415-14839512","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ec93bc","default":true}]}]}}