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Molecular Structure

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Evaluating Molecular Similarity Measures: Do Similarity Measures Reflect Electronic Structure Properties?

Journal of chemical information and modeling
The rapid adoption of big data, machine learning (ML), and generative artificial intelligence (AI) in chemical discovery has heightened the importance of quantifying molecular similarity. Molecular similarity, commonly assessed as the distance betwee...

Benzoyl Chloride Derivatization Coupled With Liquid Chromatography-Mass Spectrometry for the Simultaneous Quantification of Molnupiravir and Its Metabolite β-d-N-hydroxycytidine in Human Plasma.

Journal of separation science
A sensitive and efficient method for simultaneous quantifying molnupiravir and its active metabolite β-d-N-hydroxycytidine in human plasma was developed by combining chemical derivatization with liquid chromatography-tandem mass spectrometry. Through...

Structural Similarity, Activity, and Toxicity of Mycotoxins: Combining Insights from Unsupervised and Supervised Machine Learning Algorithms.

Journal of agricultural and food chemistry
A large number of mycotoxins and related fungal metabolites have not been assessed in terms of their toxicological impacts. Current methodologies often prioritize specific target families, neglecting the complexity and presence of co-occurring compou...

In silico discovery of novel compounds for FAK activation using virtual screening, AI-based prediction, and molecular dynamics.

Computational biology and chemistry
Focal Adhesion Kinase (FAK) is a non-receptor tyrosine kinase that plays a crucial role in cell proliferation, migration, and signal transduction. FAK is overexpressed in metastatic and advanced-stage cancers, where it is considered a key kinase in c...

Bioactive structures for inhibitors of polymerase enzyme by artificial intelligence.

Future medicinal chemistry
AIMS: Present new bioactive compounds, created by De novo Drug Design and artificial intelligence (AI), as possible inhibitors of polymerase.

A deep learning model for structure-based bioactivity optimization and its application in the bioactivity optimization of a SARS-CoV-2 main protease inhibitor.

European journal of medicinal chemistry
Bioactivity optimization is a crucial and technical task in the early stages of drug discovery, traditionally carried out through iterative substituent optimization, a process that is often both time-consuming and expensive. To address this challenge...

Discovery of naturally inspired antimicrobial peptides using deep learning.

Bioorganic chemistry
Non-ribosomal peptides (NRPs) are promising lead compounds for novel antibiotics. Bioinformatic mining of silent microbial NRPS gene clusters provide crucial insights for the discovery and de novo design of bioactive peptides. Here, we describe the e...

Sculpting molecules in text-3D space: a flexible substructure aware framework for text-oriented molecular optimization.

BMC bioinformatics
The integration of deep learning, particularly AI-Generated Content, with high-quality data derived from ab initio calculations has emerged as a promising avenue for transforming the landscape of scientific research. However, the challenge of designi...

Machine Learning-Assisted Molecular Structure Embedding for Accurate Prediction of Emerging Contaminant Removal by Ozonation Oxidation.

Environmental science & technology
Ozone has demonstrated high efficacy in depredating emerging contaminants (ECs) during drinking water treatment. However, traditional quantitative structure-activation relationship (QSAR) models often fall short in effectively normalizing and charact...

Machine Learning for Toxicity Prediction Using Chemical Structures: Pillars for Success in the Real World.

Chemical research in toxicology
Machine learning (ML) is increasingly valuable for predicting molecular properties and toxicity in drug discovery. However, toxicity-related end points have always been challenging to evaluate experimentally with respect to translation due to the re...