Neuraldecipher - reverse-engineering extended-connectivity fingerprints (ECFPs) to their molecular structures.

Chemical Science
Tuan LeDjork-Arné Clevert

Abstract

Protecting molecular structures from disclosure against external parties is of great relevance for industrial and private associations, such as pharmaceutical companies. Within the framework of external collaborations, it is common to exchange datasets by encoding the molecular structures into descriptors. Molecular fingerprints such as the extended-connectivity fingerprints (ECFPs) are frequently used for such an exchange, because they typically perform well on quantitative structure-activity relationship tasks. ECFPs are often considered to be non-invertible due to the way they are computed. In this paper, we present a fast reverse-engineering method to deduce the molecular structure given revealed ECFPs. Our method includes the Neuraldecipher, a neural network model that predicts a compact vector representation of compounds, given ECFPs. We then utilize another pre-trained model to retrieve the molecular structure as SMILES representation. We demonstrate that our method is able to reconstruct molecular structures to some extent, and improves, when ECFPs with larger fingerprint sizes are revealed. For example, given ECFP count vectors of length 4096, we are able to correctly deduce up to 69% of molecular structures on a valid...Continue Reading

References

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Dec 20, 2019·Chemical Science·Robin WinterDjork-Arné Clevert
Dec 28, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Floriane MontanariDjork-Arné Clevert

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Citations

Mar 30, 2021·Expert Opinion on Drug Discovery·José Jiménez-LunaGisbert Schneider
May 7, 2021·Rapid Communications in Mass Spectrometry : RCM·Youzhong LiuWouter Heyndrickx
Dec 22, 2020·Chemical Research in Toxicology·Hehuan MaJunzhou Huang
Aug 19, 2021·Journal of Cheminformatics·Kohulan RajanChristoph Steinbeck
Aug 29, 2021·Scientific Reports·Youngchun KwonInkoo Kim

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Software Mentioned

MELLODDY Ledger Orchestration
SMILES
ADAM optimizer
ChEMBL
SoftPlus
JECL
RDKit
Neuraldecipher
MELLODDY

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