Break down in order to build up: Decomposing small molecules for fragment-based drug design with eMolFrag

TitleBreak down in order to build up: Decomposing small molecules for fragment-based drug design with eMolFrag
Publication TypeJournal Article
Year of Publication2017
AuthorsLiu T, Naderi M, Alvin C, Mukhopadhyay S, Brylinski M
JournalJ Chem Inf Model
Volume57
Issue4
Pagination627-631
Date Published2017 Apr 24
ISSN1549-960X
Abstract

Constructing high-quality libraries of molecular building blocks is essential for successful fragment-based drug discovery. In this communication, we describe eMolFrag, a new open-source software to decompose organic compounds into nonredundant fragments retaining molecular connectivity information. Given a collection of molecules, eMolFrag generates a set of unique fragments comprising larger moieties, bricks, and smaller linkers connecting bricks. These building blocks can subsequently be used to construct virtual screening libraries for targeted drug discovery. The robustness and computational performance of eMolFrag is assessed against the Directory of Useful Decoys, Enhanced database conducted in serial and parallel modes with up to 16 computing cores. Further, the application of eMolFrag in de novo drug design is illustrated using the adenosine receptor. eMolFrag is implemented in Python, and it is available as stand-alone software and a web server at www.brylinski.org/emolfrag and https://github.com/liutairan/eMolFrag .

DOI10.1021/acs.jcim.6b00596
Alternate JournalJournal of Chemical Information and Modeling
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