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The 3D molecular structures of these compounds were downloaded from the publicly accessible electronic database, chicken BitterDB40 (http://bitterdb/dbbitter.php?mode_organism=Chicken), and prepared (through the generation of stereoisomers and protonation states at pH 7 ± 0.5) with LigPrep (version 3.6, Schrödinger, LLC, New York, NY, 2015).
All commercial compounds were downloaded as SD file format from their internal Oracle databases within AstraZeneca.
Based on the chemical data sets used in the study of Heikamp et al. [27] the same compounds were downloaded from PubChem's BioAssay database [36].
Both the NCI and the NPD databases were downloaded from the ZINC UCSF collection [57] of compounds, while the MLSMR compounds were downloaded from the PubChem database, [58] and the WDI was obtained from Thomson Reuters [59].
The TCM compounds were downloaded from TCM database (http://tcm.cmu.edu.tw/).
A total of 61,000 TCM compounds were downloaded from the TCM database (http://tcm.cmu.edu.tw/).
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The PubChem database, consisting of 473 965 compounds, was downloaded from www.ncbi.nlm.nih.gov.nih.gov
Amount of 61,000 TCM compounds was downloaded from the TCM database (http://tcm.cmu.edu.tw/); then human Ras protein (PDB ID: 4EPV) crystal structure was obtained from RCSB Protein Data Bank [ 4].
The information of interactive compounds was downloaded from STITCH (chemical_chemical.links.detailed.v3.1.tsv.gz, http://stitch.embl.de/) [ 18], a well-known database containing the interaction information of chemicals and proteins.
When COLMAR query identified a match to a compound reference spectrum present in the BMRB, HMDB, 44) or MMCD 45) databases, the reference TOCSY spectrum for the suggested compound was downloaded from the database web servers, processed in Topspin 2.0, and overlaid onto an experimental spectrum for confirmation.
Gene expression profiles of compound treatments were downloaded from Broad Institute's Connectivity Map web site (http://hRp://www.broadinsUtute.org/cmap/).org/cmap/
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