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Efficient virtual high-content screening using a distance-aware transformer model
Molecular similarity search is an often-used method in drug discovery, especially in virtual screening studies. While simple one- or two-dimensional...
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VSFlow: an open-source ligand-based virtual screening tool
Ligand-based virtual screening is a widespread method in modern drug design. It allows for a rapid screening of large compound databases in order to...
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Consensus holistic virtual screening for drug discovery: a novel machine learning model approach
In drug discovery, virtual screening is crucial for identifying potential hit compounds. This study aims to present a novel pipeline that employs...
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On the relevance of query definition in the performance of 3D ligand-based virtual screening
Ligand-based virtual screening (LBVS) methods are widely used to explore the vast chemical space in the search of novel compounds resorting to a...
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Structure and Ligand Based Virtual Screening and MPO Topological Analysis of Triazolo Thiadiazepine-fused Coumarin Derivatives as Anti-Parkinson Drug Candidates
Parkinson’s disease (PD) is a debilitating condition that can cause locomotor problems in affected patients, such as tremors and body rigidity. PD...
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Using macromolecular electron densities to improve the enrichment of active compounds in virtual screening
The quest for effective virtual screening algorithms is hindered by the scarcity of training data, calling for innovative approaches. This study...
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HDAC2 SCAN: An Expert System for Virtual Screening of Histone Deacetylase 2 Inhibitors
AbstractHistone deacetylase 2 inhibitors (HDAC2) are developed as effective drugs for the treatment of various diseases. Using various types of...
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Molecular Docking for Virtual Screening of Potential Active Ingredients in Chinese Medicines
Traditional Chinese medicine (TCM) plays a vital role in the prevention and treatment of various diseases for thousands of years. It is of great...
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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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Discovery of a novel SHP2 allosteric inhibitor using virtual screening, FMO calculation, and molecular dynamic simulation
ContextSHP2 is a non-receptor protein tyrosine phosphatase to remove tyrosine phosphorylation. Functionally, SHP2 is an essential bridge to connect...
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Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding
Many recently proposed structure-based virtual screening models appear to be able to accurately distinguish high affinity binders from non-binders....
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Efficient and knowledge-based hierarchal virtual screening applied to identify potential inhibitors of cholinesterase enzyme
Cholinesterases (ChEs) are pivotal in the pathophysiology of various neuromuscular diseases, including Parkinson’s disease, Alzheimer’s disease,...
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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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Virtual Screening, Molecular Docking Studies and DFT Calculations of Novel Anticancer Flavonoids as Potential VEGFR-2 Inhibitors
Angiogenesis is one of the hallmarks of cancer that helps in the development of new abnormal blood vessels from preexisting blood vessels. The key...
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Structure-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation of EGFR for the Clinical Treatment of Glioblastoma
Glioblastoma (GBM) is a WHO Grade IV tumor with poor visibility, a high risk of comorbidity, and exhibit limited treatment options. Resurfacing from...
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Iterative machine learning-based chemical similarity search to identify novel chemical inhibitors
Machine learning-based chemical screening has made substantial progress in recent years. However, these predictions often have low accuracy and high...
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Identifying and characterising promising small molecule inhibitors of kinesin spindle protein using ligand-based virtual screening, molecular docking, molecular dynamics and MM‑GBSA calculations
The kinesin spindle protein (Eg5) is a mitotic protein that plays an essential role in the formation of the bipolar spindles during the mitotic...
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Discovery of novel S6K1 inhibitors by an ensemble-based virtual screening method and molecular dynamics simulation
Ribosomal protein S6 kinase beta-1 (S6K1) is considered a potential target for the treatment of various diseases, such as obesity, type II diabetes,...
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Fragment-based virtual screening discovers potential new Plasmodium PI4KIIIβ ligands
Type III beta phosphatidylinositol 4-kinase (PI4KIIIβ) is the only clinically validated drug target in Plasmodium kinases and therefore a critical...
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Pharmacophore-based virtual screening from phytocannabinoids as antagonist r-CB1
Search for new pharmacological alternatives for obesity is based on the design and development of compounds that can aid in weight loss so that they...
