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...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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BMC
2021-11-01
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| Series: | Journal of Cheminformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13321-021-00566-4 |
| _version_ | 1819004554257104896 |
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| author | Francois Berenger Koji Tsuda |
| author_facet | Francois Berenger Koji Tsuda |
| author_sort | Francois Berenger |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-20T23:38:44Z |
| format | Article |
| id | doaj.art-5439dd3838a54210ab3db8f99d806114 |
| institution | Directory Open Access Journal |
| issn | 1758-2946 |
| language | English |
| last_indexed | 2024-12-20T23:38:44Z |
| publishDate | 2021-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Cheminformatics |
| spelling | doaj.art-5439dd3838a54210ab3db8f99d8061142022-12-21T19:23:09ZengBMCJournal of Cheminformatics1758-29462021-11-0113111010.1186/s13321-021-00566-4Molecular generation by Fast Assembly of (Deep)SMILES fragmentsFrancois Berenger0Koji Tsuda1Graduate School of Frontier Sciences, The University of TokyoGraduate School of Frontier Sciences, The University of TokyoAbstract 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.https://doi.org/10.1186/s13321-021-00566-4Molecular generationMolecular fragmentsSMILESDeepSMILES |
| spellingShingle | Francois Berenger Koji Tsuda Molecular generation by Fast Assembly of (Deep)SMILES fragments Journal of Cheminformatics Molecular generation Molecular fragments SMILES DeepSMILES |
| title | 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_short | Molecular generation by Fast Assembly of (Deep)SMILES fragments |
| title_sort | molecular generation by fast assembly of deep smiles fragments |
| topic | Molecular generation Molecular fragments SMILES DeepSMILES |
| url | https://doi.org/10.1186/s13321-021-00566-4 |
| work_keys_str_mv | AT francoisberenger moleculargenerationbyfastassemblyofdeepsmilesfragments AT kojitsuda moleculargenerationbyfastassemblyofdeepsmilesfragments |