Instead, finding a common reference shape triggers computing, via Eq. 2, the shape Tanimoto between the query conformer and database conformer, as may be performed by a typical brute-force ROCS approach.
The alignment between the query conformer and database conformer is determined using the retained rotational matrices and translational vectors relative to that reference shape.
C Conformer Multiple conformer, All-conformer-pair approach Similarity scores that one may expect when a single "query" conformer is compared to a set of multiple diverse conformers of the "database" compounds, using the "all-conformer-pair" approach.
D Conformer Multiple conformer, Best-conformer-pair approach Similarity scores that one may expect when a single "query" conformer is compared to a set of multiple diverse conformers of the "database" compounds using the "best-conformer-pair" approach.
E Compound Multiple conformer, Best-conformer-pair approach Similarity scores that one may expect when each "query" conformer is compared to a set of multiple diverse conformers of the "database" compounds using the "best-conformer-pair" approach.
B Compound Multiple conformer, All-conformer-pair approach Similarity scores that one may expect when each "query" conformer is compared to a set of multiple diverse conformers of the "database" compounds, using the "all-conformer-pair" approach.
In contrast to ROCS, AR can only occur when the query conformer structure is found to have a reference shape in common with a database conformer.
The alignment-recycling (AR) methodology is intended to obviate performing the optimization required to maximize the volume overlap of the query conformer to each and every conformer in a 3D conformer dataset.
In these cases, a 3-D lattice of points separated by 0.25 Å give the shape overlap of a carbon probe-atom at the grid point to the query conformer.
A cut-off distance of 4.5 Å is used for each query conformer atom, where no additional contribution to shape overlap is considered.
