Molecular generation by Fast Assembly of (Deep)SMILES fragments

Abstract Background In recent years, in silico molecular design is regaining interest. To generate on a computer molecules with optimized properties, scoring functions can be coupled with a molecular generator to design novel molecules with a desired property profile. Results In this article, a simp...

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Autores principales:	Francois Berenger, Koji Tsuda
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Molecular generation Molecular fragments SMILES DeepSMILES Information technology T58.5-58.64 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/5439dd3838a54210ab3db8f99d806114
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spelling	oai:doaj.org-article:5439dd3838a54210ab3db8f99d8061142021-11-21T12:33:31ZMolecular generation by Fast Assembly of (Deep)SMILES fragments10.1186/s13321-021-00566-41758-2946https://doaj.org/article/5439dd3838a54210ab3db8f99d8061142021-11-01T00:00:00Zhttps://doi.org/10.1186/s13321-021-00566-4https://doaj.org/toc/1758-2946Abstract Background In recent years, in silico molecular design is regaining interest. To generate on a computer molecules with optimized properties, scoring functions can be coupled with a molecular generator to design novel molecules with a desired property profile. Results In this article, a simple method is described to generate only valid molecules at high frequency ( $$>300,000$$ > 300 , 000 molecule/s using a single CPU core), given a molecular training set. The proposed method generates diverse SMILES (or DeepSMILES) encoded molecules while also showing some propensity at training set distribution matching. When working with DeepSMILES, the method reaches peak performance ( $$>340,000$$ > 340 , 000 molecule/s) because it relies almost exclusively on string operations. The “Fast Assembly of SMILES Fragments” software is released as open-source at https://github.com/UnixJunkie/FASMIFRA . Experiments regarding speed, training set distribution matching, molecular diversity and benchmark against several other methods are also shown.Francois BerengerKoji TsudaBMCarticleMolecular generationMolecular fragmentsSMILESDeepSMILESInformation technologyT58.5-58.64ChemistryQD1-999ENJournal of Cheminformatics, Vol 13, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Molecular generation Molecular fragments SMILES DeepSMILES Information technology T58.5-58.64 Chemistry QD1-999
spellingShingle	Molecular generation Molecular fragments SMILES DeepSMILES Information technology T58.5-58.64 Chemistry QD1-999 Francois Berenger Koji Tsuda Molecular generation by Fast Assembly of (Deep)SMILES fragments
description	Abstract Background In recent years, in silico molecular design is regaining interest. To generate on a computer molecules with optimized properties, scoring functions can be coupled with a molecular generator to design novel molecules with a desired property profile. Results In this article, a simple method is described to generate only valid molecules at high frequency ( $$>300,000$$ > 300 , 000 molecule/s using a single CPU core), given a molecular training set. The proposed method generates diverse SMILES (or DeepSMILES) encoded molecules while also showing some propensity at training set distribution matching. When working with DeepSMILES, the method reaches peak performance ( $$>340,000$$ > 340 , 000 molecule/s) because it relies almost exclusively on string operations. The “Fast Assembly of SMILES Fragments” software is released as open-source at https://github.com/UnixJunkie/FASMIFRA . Experiments regarding speed, training set distribution matching, molecular diversity and benchmark against several other methods are also shown.
format	article
author	Francois Berenger Koji Tsuda
author_facet	Francois Berenger Koji Tsuda
author_sort	Francois Berenger
title	Molecular generation by Fast Assembly of (Deep)SMILES fragments
title_short	Molecular generation by Fast Assembly of (Deep)SMILES fragments
title_full	Molecular generation by Fast Assembly of (Deep)SMILES fragments
title_fullStr	Molecular generation by Fast Assembly of (Deep)SMILES fragments
title_full_unstemmed	Molecular generation by Fast Assembly of (Deep)SMILES fragments
title_sort	molecular generation by fast assembly of (deep)smiles fragments
publisher	BMC
publishDate	2021
url	https://doaj.org/article/5439dd3838a54210ab3db8f99d806114
work_keys_str_mv	AT francoisberenger moleculargenerationbyfastassemblyofdeepsmilesfragments AT kojitsuda moleculargenerationbyfastassemblyofdeepsmilesfragments
_version_	1718418942599364608

Molecular generation by Fast Assembly of (Deep)SMILES fragments

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