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2017 ; 57
(4
): 627-631
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Break Down in Order To Build Up: Decomposing Small Molecules for Fragment-Based
Drug Design with eMolFrag
#MMPMID28346786
Liu T
; Naderi M
; Alvin C
; Mukhopadhyay S
; Brylinski M
J Chem Inf Model
2017[Apr]; 57
(4
): 627-631
PMID28346786
show ga
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 .