In building the rotamer library, all instances of every fragment are collected in the molecular database using a graph isomorphism search [29].
The compounds were imported into a molecular database using the Molecular Operating Environment MOEE) version 2012 [ 44].
GSEA was run in preranked mode using the Gene Ontology (GO) set (C5) and curated gene sets (C2) from the Molecular Signatures Database using 1000 permutations to estimate the false discovery rate to assess statistical significance.
We linked every gene family with information from the KEGG molecular pathways database using a Blast search against the database.
In order to assess the biological significance of this signature, it was compared to 5562 gene sets in the Broad Molecular Signature Database using Gene Set Enrichment Analysis (GSEA).
Perform a molecular formula search against each of the databases using a suitable threshold value (Δthres = σ, 1.5σ, or 2σ).
Notable among these were several amino acids, none of which were found in the extensive molecular mass database used in our previous study [ 8].
We calculated 2D molecular structure similarity between all the drugs in each database using a 2D molecular fingerprint called MACCS.
In addition to 2D similarity searching, 3D similarity searching is provided on Pub3D database using 12-dimensional molecular shape descriptors [20] calculated for our Pub3D database of 3D minimized structures of PubChem compounds.
Multiple alignments of sequences and the evolutionary history were deduced with other sequences downloaded from the GenBank database using Mega 6 (Molecular evolutionary genetic analysis) software (Tamura et al. 2013).
