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What is ATOM?

ATOM is one of the pre-calculated SUBSTRUCTURE types. ATOM entries are distinguished by their elements and by their electrostatic and physicochemical properties, which are calculated for each non-hydrogen atom of each compound. Hydrogen atoms are not assigned individual ATOM entries, but are included with their adjacent non-hydrogen atoms. ATOM entries can be searched using Substructure Search option.

Here are the ATOM entries for C, O, N, S and P, that have the most numbers in this database:

Physicochemical and Electrochemical Properties

Physicochemical and electrochemical properties are defined in each ATOM entry, and can be used in the BiSSCat Structure Search option. Most of these properties (excluding ring properties) are based on the programmable atom typer program, PATTY (Bush and Sheridan, 1993).

Note that the physicochemical properties are provided for each non-hydrogen atom (ATOM entry) rather than for the total structure of the chemical compound. For example, while ethanol (CH3CH2OH) is a hydrophilic molecule, using the PATTY method, the two carbon atoms of the ethyl group (CH3CH2-) and the oxygen atom of the hydroxy group (-OH) are assigned as being "hydrophobic" and "polar", respectively.

BiSSCat v1.07.31
Developed by Masaaki Kotera, Department of Biochemistry, Trinity College Dublin.
Science Foundation of Ireland is gratefully acknowledged.