title: Break Down in Order To Build Up: Decomposing Small Molecules for Fragment-Based Drug Design with eMolFrag.
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 .
authors.forename: Tairan
authors.initials: T
authors.lastname: Liu
authors.forename: Misagh
authors.initials: M
authors.lastname: Naderi
authors.affiliation: Department of Computer Science and Information Systems, Bradley University , Peoria, Illinois 61625, United States.
authors.forename: Chris
authors.initials: C
authors.lastname: Alvin
authors.forename: Supratik
authors.initials: S
authors.lastname: Mukhopadhyay
authors.forename: Michal
authors.identifier: 0000-0002-6204-2869
authors.initials: M
authors.lastname: Brylinski
mesh_terms: D016208:Databases, Factual; D015195:Drug Design; D008958:Models, Molecular; D008968:Molecular Conformation; D058915:Purinergic P1 Receptor Antagonists / Q000737:chemistry / Q000494:pharmacology; D018047:Receptors, Purinergic P1 / Q000378:metabolism; D012984:Software
chemical_list: D058915:Purinergic P1 Receptor Antagonists; D018047:Receptors, Purinergic P1