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Comparative Glycomics Analysis of Mass Spectrometry Data
Glycan profiling is a common strategy that is used to determine the distribution of N-linked glycans, O-linked glycans and glycolipid associated...
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FastGrow: on-the-fly growing and its application to DYRK1A
Fragment-based drug design is an established routine approach in both experimental and computational spheres. Growing fragment hits into viable...
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Development of an open-source software for isomer enumeration
This article documents enu , a freely-downloadable, open-source and stand-alone program written in C++ for the enumeration of the constitutional...
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Evolution of the structural and electronic properties of AlnP13−n (n = 0–13) clusters
We perform calculations for the most stable structures of Al n P 13− n semiconductor binary clusters with n = 0–13 by using genetic algorithm combined...
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MERMAID: an open source automated hit-to-lead method based on deep reinforcement learning
The hit-to-lead process makes the physicochemical properties of the hit molecules that show the desired type of activity obtained in the screening...
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Discovery of potent inhibitors of α-synuclein aggregation using structure-based iterative learning
Machine learning methods hold the promise to reduce the costs and the failure rates of conventional drug discovery pipelines. This issue is...
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COCONUT online: Collection of Open Natural Products database
Natural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries as many of...
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Assessing the performance of docking, FEP, and MM/GBSA methods on a series of KLK6 inhibitors
Kallikrein 6 (KLK6) is an attractive drug target for the treatment of neurological diseases and for various cancers. Herein, we explore the accuracy...
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Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores
Fragment spaces are an efficient way to model large chemical spaces using a handful of small fragments and a few connection rules. The development of...
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Microbial Metabolites Annotation by Mass Spectrometry-Based Metabolomics
Since the discovery of penicillin, microbial metabolites have been extensively investigated for drug discovery purposes. In the last decades,...
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Prediction of organic compound aqueous solubility using machine learning: a comparison study of descriptor-based and fingerprints-based models
A reliable and practical determination of a chemical species’ solubility in water continues to be examined using empirical observations and...
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Automatic anomaly detection in engineering diagrams using machine learning
This study implements a method of automating anomaly detection in engineering diagrams by extracting patterns within graphs after recognizing graphs...
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In silico prediction models for thyroid peroxidase inhibitors and their application to synthetic flavors
Systematic toxicity tests are often waived for the synthetic flavors as they are added in a very small amount in foods. However, their safety for...
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Maximum common property: a new approach for molecular similarity
The maximum common property similarity (MCPhd) method is presented using descriptors as a new approach to determine the similarity between two...
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Probabilistic generative transformer language models for generative design of molecules
Self-supervised neural language models have recently found wide applications in the generative design of organic molecules and protein sequences as...
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Biotransformation of 1-nitro-2-phenylethane \(\longrightarrow \) 2-phenylethanol from fungi species of the Amazon biome: an experimental and theoretical analysis
ContextNatural products and their biotransformation procedures are a powerful source of new chromophores with potential applications in fields like...
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Molecular fragmentation as a crucial step in the AI-based drug development pathway
The AI-based small molecule drug discovery has become a significant trend at the intersection of computer science and life sciences. In the pursuit...
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Machine learning approaches to optimize small-molecule inhibitors for RNA targeting
In the era of data science, data-driven algorithms have emerged as powerful platforms that can consolidate bioisosteric rules for preferential...
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Valorization of Boehmeria nivea stalk towards multipurpose fractionation: furfural, pulp, and phenolic monomers
BackgroundAs one of the most abundant bioresource in nature, the value-added utilization of lignocellulosic biomass is limited due to its inherent...
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Discovering New Natural Products Using Metabolomics-Based Approaches
The incessant search for new natural molecules with biological activities has forced researchers in the field of chemistry of natural products to...