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Research Article

Novel Canonical Coding Method for Representation of Three-Dimensional Structures

Hiroko Satoh,*^†^‡^§ Hiroyuki Koshino,*^‡ Kimito Funatsu, and Tadashi Nakata^‡

RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan, PRESTO, Japan Science and Technology Corporation, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Department of Knowledge-Based Information Engineering, Toyohashi University of Technology, Tempaku, Toyohashi, Aichi 441-8580, Japan

J. Chem. Inf. Comput. Sci., 2000, 40 (3), pp 622–630

DOI: 10.1021/ci990147d

Publication Date (Web): April 29, 2000

Corresponding authors.

†

Telephone: 048-462-1111 (ext. 3449). E-mail: hsatoh@ postman.riken.go.jp.

‡

RIKEN.

PRESTO.

Telephone: 048-462-1111 (ext. 3031). E-mail: koshino@ postman.riken.go.jp.

Toyohashi University of Technology.

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.

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