Maximum common property: a new approach for molecular similarity

Journal of Cheminformatics

Gonzalo Cerruela-García¹  Nicolás García-Pedrajas¹  Ramón Carrasco-Velar²  Aurelio Antelo-Collado² 

[1] Department of Computing and Numerical Analysis, University of Cordoba, Campus de Rabanales, Albert Einstein Building, E-14071, Córdoba, Spain;University of Informatics Science, Carretera San Antonio de los Baños Km. 2 1/2 , Boyeros, La Habana, Cuba, Havana, Cuba;

关键词: Maximum common property;    Electrotopographic state index;    Molecular similarity;    Tanimoto function;    Maximum common structure;   

DOI  :  10.1186/s13321-020-00462-3

来源: Springer

【 摘 要 】

The maximum common property similarity (MCPhd) method is presented using descriptors as a new approach to determine the similarity between two chemical compounds or molecular graphs. This method uses the concept of maximum common property arising from the concept of maximum common substructure and is based on the electrotopographic state index for atoms. A new algorithm to quantify the similarity values of chemical structures based on the presented maximum common property concept is also developed in this paper. To verify the validity of this approach, the similarity of a sample of compounds with antimalarial activity is calculated and compared with the results obtained by four different similarity methods: the small molecule subgraph detector (SMSD), molecular fingerprint based (OBabel_FP2), ISIDA descriptors and shape-feature similarity (SHAFTS). The results obtained by the MCPhd method differ significantly from those obtained by the compared methods, improving the quantification of the similarity. A major advantage of the proposed method is that it helps to understand the analogy or proximity between physicochemical properties of the molecular fragments or subgraphs compared with the biological response or biological activity. In this new approach, more than one property can be potentially used. The method can be considered a hybrid procedure because it combines descriptor and the fragment approaches.

【 授权许可】

CC BY