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Spatial chemical distance based on atomic property fields A. V. Grigoryan I. Kufareva M. Totrov
 

Summary: Spatial chemical distance based on atomic property fields
A. V. Grigoryan I. Kufareva M. Totrov
R. A. Abagyan
Received: 20 September 2009 / Accepted: 6 December 2009 / Published online: 13 March 2010
The Author(s) 2010. This article is published with open access at Springerlink.com
Abstract Similarity of compound chemical structures
often leads to close pharmacological profiles, including
binding to the same protein targets. The opposite, however,
is not always true, as distinct chemical scaffolds can
exhibit similar pharmacology as well. Therefore, relying on
chemical similarity to known binders in search for novel
chemicals targeting the same protein artificially narrows
down the results and makes lead hopping impossible. In
this study we attempt to design a compound similarity/
distance measure that better captures structural aspects of
their pharmacology and molecular interactions. The mea-
sure is based on our recently published method for com-
pound spatial alignment with atomic property fields as a
generalized 3D pharmacophoric potential. We optimized
contributions of different atomic properties for better dis-

  

Source: Abagyan, Ruben - School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego

 

Collections: Biology and Medicine