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RetroRanker: leveraging reaction changes to improve retrosynthesis prediction through re-ranking
Retrosynthesis is an important task in organic chemistry. Recently, numerous data-driven approaches have achieved promising results in this task....
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Improving the performance of models for one-step retrosynthesis through re-ranking
AbstractRetrosynthesis is at the core of organic chemistry. Recently, the rapid growth of artificial intelligence (AI) has spurred a variety of novel...
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Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations
Identifying bioactive conformations of small molecules is an essential process for virtual screening applications relying on three-dimensional...
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Description of the updated nutrition calculation of the Oxford WebQ questionnaire and comparison with the previous version among 207,144 participants in UK Biobank
PurposeThe Oxford WebQ is a web-based 24-h dietary assessment method which has been used in UK Biobank and other large prospective studies. The food...
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In silico assessment of natural products and approved drugs as potential inhibitory scaffolds targeting aminoacyl-tRNA synthetases from Plasmodium
Malaria remains the leading cause of deaths globally, despite significant advancement towards understanding its epidemiology and availability of...
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Erosion patterns, drainage dynamics, and their environmental implications: a case study of the hammamet basin using advanced geospatial and morphometric analysis
Understanding erosion patterns and drainage conditions is crucial for optimizing agricultural productivity and for addressing the challenges of...
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ChemFlow_py: a flexible toolkit for docking and rescoring
The design of accurate virtual screening tools is an open challenge in drug discovery. Several structure-based methods have been developed at...
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Rubrolide analogues as urease inhibitors
Urease is an important virulence factor involved in the colonization and infection of gastric mucosa by Helicobacter pylori . In this work, the urease...
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Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets
With the increasingly more important role of machine learning (ML) models in chemical research, the need for putting a level of confidence to the...
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Modeling the expansion of virtual screening libraries
Recently, ‘tangible’ virtual libraries have made billions of molecules readily available. Prioritizing these molecules for synthesis and testing...
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Structural annotation of unknown molecules in a miniaturized mass spectrometer based on a transformer enabled fragment tree method
Structural annotation of small molecules in tandem mass spectrometry has always been a central challenge in mass spectrometry analysis, especially...
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SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces
AbstractThe growing size of make-on-demand chemical libraries is posing new challenges to cheminformatics. These ultra-large chemical libraries...
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Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: I. Standard procedure
Despite the massive application of end-point free energy methods in protein–ligand and protein–protein interactions, computational understandings...
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The application of multi-elemental fingerprints and chemometrics for discriminating between cage and free-range table eggs based on atomic absorption spectrometry (AAS) and colorimetry
Mislabeling is a common fraudulent activity in food marketing as producers take advantage of rising demand for ethically produced, high quality...
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Protein-Protein Docking Approach to GPCR Oligomerization
G-protein-coupled receptors (GPCRs), the largest family of human membrane proteins, play a crucial role in cellular control and are the target of...
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Research Progress of ARTP Mutagenesis Technology Based on Citespace Visualization Analysis
Atmospheric and room temperature plasma (ARTP) mutagenesis technology has been developed rapidly in recent years because of its simple operation,...
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Hybrid wastewater treatment and reuse enhances urban water system resilience to disruptive incidents
Water and wastewater systems are critical infrastructure whose disruption directly threatens public health, economic growth and the reliability and...
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Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design
Systematic optimization of large macrocyclic peptide ligands is a serious challenge. Here, we describe an approach for lead-optimization using the...
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Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant
End-point free energy calculations as a powerful tool have been widely applied in protein–ligand and protein–protein interactions. It is often...
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Covalent docking in CDOCKER
Targeted covalent inhibitors (TCIs) are considered to be an important component in the toolbox of drug discovery and about 30% of currently marketed...
