Novel Canonical Coding Method for Representation of Three-Dimensional Structures

Abstract

A new canonical coding method for representation of three-dimensional structures, CAST (CAnonical representation of STereochemistry), is described. CAST canonically codes stereochemistry around an atom in a molecule. The same CAST notations are given for atoms of molecules in the same conformation. The CAST code is based on the dihedral angles of four atoms that are uniquely defined by a molecular tree structure. CAST has successfully represented similarities and differences between several conformers.

Privileged Structures - Dream or Reality: Preferential Organization of Azanaphthalene Scaffold

“…The 2D-based procedure of finding a particular molecular motif can be performed using a regular expression approach (SMARTS) as well [180]. The transformation of the molecular (sub)graph representation into its canonically coded linear atoms/bonds specification enables massive substructure recognitions [181]. Typically, the substructures might be represented by exact and/or fuzzy linear/branched/cyclic motifs where nonhydrogen atoms are encoded symbolically with wildcards.…”

Mapping Fragmental Drug-Likeness in the MoStBioDat Environment:Intramolecular Hydrogen Bonding Motifs in β-Ketoenols

“…The procedure of finding a particular molecular motif might be performed using a regular expression approach (SMARTS) as well. The transformation of the molecular graph representation into its canonically-coded linear atoms/bonds specification enables massive substructure to be recognized [14,15].…”

Extended CAST Coding Method for Exact Search of Stereochemical Structures

“…The relationships between codes in the molecular tree are translated to linear notations using some separator codes, a semi-colon, a comma, and an asterisk as mentioned above, according to the CAST coding rule. 7,8 In Figure 3, the notations that related to R and S-configurations are bold-and double-underlined, respectively. In the notations from C1, the absolute configurational difference for C3 and C4 are represented, and in the notations from C4, the differences for C2 are represented.…”

“…Some coding methods for three-dimensional chemical structures have been developed and used for structural representation in some chemical software, however, an essential problem of exact search of structures considering configurational and conformational structural environments has been remained. [1][2][3][4][5][6] We reported CAST (CAnonical-representation of STereochemistry) coding method in the previous paper 7,8 . The basic CAST gives canonical codes based on the dihedral angles.…”