The molecules are annotated with properties such as description, target, format, bioassay, molecular weight, hydrogen bond donor, hydrogen bond acceptor and rotatable bond.
The concept of chemical space, whereby molecules are annotated with a set of quantitative molecular properties and placed in a high-dimensional property space with each dimension corresponding to a different property, offers a practical approach to represent the structural diversity of large molecule collections [1 28].
A total of 56 molecules are annotated as affecting neoplasia and eight of these are dysregulated over 1.5 fold in Ad12-TC compared to Ad5-TC: down-regulation of ATM, CD19, CD3G, GADD45B, HPSE, TFAP2A and TFPI was observed, whereas levels of EGFR were found to be up-regulated (Additional file 1).
If the ligand has fewer than two consecutive peptide bonds (examples of this include several PPACK inhibitors and other peptide-like molecules), it is annotated as a non-polymer like any other small molecule in the CCD, but with an identifiable subcomponent sequence running from amino terminal (N) to carboxy (C) terminal.
Depending on the kind of the PhysicalEntity, i.e. if it is a protein, complex, DNA, RNA or small molecule, the species is annotated with the corresponding SBO term (Courtot et al., 2011).
Each of the >7000 small molecule and peptide ligands is annotated with manually curated 2D chemical structures or amino acid sequences, nomenclature and links to external resources for further information.
Reverse is annotated by Fries.
The list of biologically relevant genes is annotated using homology to targets of approved pharmaceuticals; the molecular and cellular properties of any existing published active small molecules; three-dimensional (3D) structure, druggability or ligandability; and functional class and subcellular localization.
Image quality is annotated for each image.
EFTUD2 is annotated as a spliceosome component.
