We note that the optimal box size is calculated directly from the R g of a docking ligand, thus it can be obtained for an arbitrary compound.
Manually constructed classifications may furthermore be far from complete in the sense that an arbitrary compound belongs to a vast number of classes yet will only have been classified under one or two - those deemed to be the most relevant.
Given significant substructure pairs, for an arbitrary compound-protein (graph-sequence) pair, we can compute a binary vector of 10,000 elements where if a significant substructure pair is included, the value of the corresponding element is 1; otherwise zero.
The scalability of GRASP fingerprints on finding the most similar drug-target pair to an arbitrary given compound-protein (graph-sequence) pair was examined by generating 975,243,103 compound-protein pairs (which we call MASS) from 140,937 bioactive compounds and 6,919 druggable proteins (Methods section and Methods S1).
However, both approaches require a somewhat arbitrary classification of compounds that may result in the loss of useful information.
With this in mind, each library was evaluated with respect to its similarity to known (arbitrary selected) active compound(s).
Based on an arbitrary prediction, all compound mutant mice had no more than 93.75% genetic background of the C57BL/6J strain and at least 6.25% genetic background of the AJ strain.
Fortunately, while CoMFA restricts training molecule diversity in order to get meaningful overlays, 2D-FPT models can (and should!) be trained on sets of compounds of arbitrary diversity – addition of assumed inactive random compounds to the structurally homogeneous thrombin inhibitor series produced models that successfully extrapolate to molecules of different topology.
One other parameter that we assessed was the arbitrary definition of active compounds as IC50 <50 μ m, which might be considered a generous cutoff.
The viewer allows any arbitrary set of 3-D conformersorformers or conformer pairs (substance and compound) that exists within PubChem to be viewed or superimposed.
