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MacFrag: segmenting large-scale molecules to obtain diverse fragments with high qualities

SUMMARY: Construction of high-quality fragment libraries by segmenting organic compounds is an important part of the drug discovery paradigm. This article presents a new method, MacFrag, for efficient molecule fragmentation. MacFrag utilized a modified version of BRICS rules to break chemical bonds...

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Detalles Bibliográficos
Autores principales: Diao, Yanyan, Hu, Feng, Shen, Zihao, Li, Honglin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9872447/
https://www.ncbi.nlm.nih.gov/pubmed/36637187
http://dx.doi.org/10.1093/bioinformatics/btad012
Descripción
Sumario:SUMMARY: Construction of high-quality fragment libraries by segmenting organic compounds is an important part of the drug discovery paradigm. This article presents a new method, MacFrag, for efficient molecule fragmentation. MacFrag utilized a modified version of BRICS rules to break chemical bonds and introduced an efficient subgraphs extraction algorithm for rapid enumeration of the fragment space. The evaluation results with ChEMBL dataset exhibited that MacFrag was overall faster than BRICS implemented in RDKit and modified molBLOCKS. Meanwhile, the fragments acquired through MacFrag were more compliant with the ‘Rule of Three’. AVAILABILITY AND IMPLEMENTATION: https://github.com/yydiao1025/MacFrag. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.