By utilizing the 3 × 3 rotational matrix and XYZ translational vector that align a 3-D chemical structure conformer to a common reference shape (retained after shape fingerprint generation), one could generate a superposition between conformers for each common reference shape.
Second, a multiple co-inertia analysis (MCOA) was performed, which reveals the common features of single-marker analyses, builds a reference structure and makes it possible to compare single-marker structures with this reference through graphical tools.
This fundamental problem in structural biology is commonly addressed by performing a superposition, which removes arbitrary differences in translation and rotation so that a set of structures is oriented in a common reference frame (Flower, 1999).
A common reference specification for standardisation would be of immense value in interoperability between structure repositories as well as between toolkits (though the latter is still confounded by differences in lower level cheminformatic features such as aromaticity models).
This was achieved by recognizing that two chemical structure conformers with similar 3-D shape align to a common reference shape in a similar fashion.
Several standards are required to produce the functional and semantic interoperability necessary to support the exchange of such data: a common reference information model, a common set of data elements, a common terminology, common data structures, and a common transport standard.
It only considered relatively small (<28 non-hydrogen atoms) and inflexible (<6 rotatable bonds) chemical structures and would not compute any shape similarity value when there was no common reference shape.
The most common approach, which we study in this paper, uses molecules characterised by 2D fingerprints, with the similarity between a reference structure and a database structure calculated using an association coefficient such as the Tanimoto coefficient [1, 8].
"Lynch mob," I believe, was a common reference.
