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Small Molecule Libraries

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Machine learning assisted in Silico discovery and optimization of small molecule inhibitors targeting the Nipah virus glycoprotein.

Scientific reports 40341732
The Nipah virus (NiV), a lethal pathogen from the Paramyxoviridae family, presents a significant global health threat as a result of its high mortality rate and inter-human transmission. This investigation employed in silico methods that were assiste...
Antiviral Agents Computer Simulation Drug Discovery Glycoproteins Humans Machine Learning Molecular Docking Simulation Molecular Dynamics Simulation Nipah Virus Small Molecule Libraries Viral Proteins
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A Database for Large-Scale Docking and Experimental Results.

Journal of chemical information and modeling 40273444
The rapid expansion of readily accessible compounds over the past six years has transformed molecular docking, improving hit rates and affinities. While many millions of molecules may score well in a docking campaign, the results are rarely fully sha...
Databases, Factual Ligands Machine Learning Molecular Docking Simulation Proteins Small Molecule Libraries
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Predicting Antimicrobial Class Specificity of Small Molecules Using Machine Learning.

Journal of chemical information and modeling 39987507
While the useful armory of antibiotic drugs is continually depleted due to the emergence of drug-resistant pathogens, the development of novel therapeutics has also slowed down. In the era of advanced computational methods, approaches like machine le...
Anti-Bacterial Agents Anti-Infective Agents Bacteria Drug Discovery Machine Learning Microbial Sensitivity Tests Small Molecule Libraries
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Identifying RNA-small Molecule Binding Sites Using Geometric Deep Learning with Language Models.

Journal of molecular biology 39961524
RNAs are emerging as promising therapeutic targets, yet identifying small molecules that bind to them remains a significant challenge in drug discovery. This underscores the crucial role of computational modeling in predicting RNA-small molecule bind...
Binding Sites Computational Biology Deep Learning Drug Discovery Models, Molecular Nucleic Acid Conformation RNA Small Molecule Libraries
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Discovery of TRPV4-Targeting Small Molecules with Anti-Influenza Effects Through Machine Learning and Experimental Validation.

International journal of molecular sciences 39941149
Transient receptor potential vanilloid 4 (TRPV4) is a calcium-permeable cation channel critical for maintaining intracellular Ca homeostasis and is essential in regulating immune responses, metabolic processes, and signal transduction. Recent studies...
Animals Antiviral Agents Drug Discovery Humans Influenza A virus Influenza, Human Machine Learning Mice Molecular Docking Simulation Orthomyxoviridae Infections Small Molecule Libraries TRPV Cation Channels
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Prediction of Chromatographic Retention Time of a Small Molecule from SMILES Representation Using a Hybrid Transformer-LSTM Model.

Journal of chemical information and modeling 40152775
Accurate retention time (RT) prediction in liquid chromatography remains a significant consideration in molecular analysis. In this study, we explore the use of a transformer-based language model to predict RTs by treating simplified molecular input ...
Chromatography, High Pressure Liquid Chromatography, Reverse-Phase Neural Networks, Computer Small Molecule Libraries Time Factors
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Leveraging Transfer Learning for Predicting Protein-Small-Molecule Interaction Predictions.

Journal of chemical information and modeling 40127309
A complex web of intermolecular interactions defines and regulates biological processes. Understanding this web has been particularly challenging because of the sheer number of actors in biological systems: ∼10 proteins in a typical human cell offer ...
Humans Ligands Machine Learning Neural Networks, Computer Protein Binding Proteins Small Molecule Libraries
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Rapid traversal of vast chemical space using machine learning-guided docking screens.

Nature computational science 40082701
The accelerating growth of make-on-demand chemical libraries provides unprecedented opportunities to identify starting points for drug discovery with virtual screening. However, these multi-billion-scale libraries are challenging to screen, even for ...
Algorithms Drug Discovery Humans Ligands Machine Learning Molecular Docking Simulation Receptors, G-Protein-Coupled Small Molecule Libraries
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A dataset for machine learning-based QSAR models establishment to screen beta-lactamase inhibitors using the FARM -BIOMOL chemical library.

BMC research notes 40033358
OBJECTIVES: Beta-lactamase is a bacterial enzyme that deactivates beta-lactam antibiotics, and it is one of the leading causes of antibiotic resistance problems globally. In current drug discovery research, molecular simulation, like molecular dockin...
beta-Lactamase Inhibitors beta-Lactamases Databases, Chemical Machine Learning Molecular Docking Simulation Quantitative Structure-Activity Relationship Small Molecule Libraries
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PROFIS: Design of Target-Focused Libraries by Probing Continuous Fingerprint Space with Recurrent Neural Networks.

Journal of chemical information and modeling 40293047
This study introduces PROFIS, a new generative model capable of the design of structurally novel and target-focused compound libraries. The model relies on a recurrent neural network that was trained to decode embedded molecular fingerprints into SMI...
Bayes Theorem Drug Design Ligands Neural Networks, Computer Receptors, Dopamine D2 Recurrent Neural Networks Small Molecule Libraries
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