ArticleJournal of computational chemistry2014
Shape-based virtual screening with volumetric aligned molecular shapes.
Article in Journal of computational chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Prioritizing neuroactive ligands using motif-guided virtual discovery and zebrafish profiling.npj drug discovery · 2026Article
- Prioritizing Neuroactive Ligands Using Motif-Guided Virtual Discovery and Zebrafish Profiling.bioRxiv : the preprint server for biology · 2026Article
- Navigating structure-based drug discovery with emerging innovations in physics- and knowledge-based approaches.npj drug discovery · 2025Review
- AutoDock-SS: AutoDock for Multiconformational Ligand-Based Virtual Screening.Journal of chemical information and modeling · 2024Article
- On the Value of Using 3D Shape and Electrostatic Similarities in Deep Generative Methods.Journal of chemical information and modeling · 2022Article
- Applications of Virtual Screening in Bioprospecting: Facts, Shifts, and Perspectives to Explore the Chemo-Structural Diversity of Natural Products.Frontiers in chemistry · 2021Review
- Virtual Screening for Potential Inhibitors of Human Hexokinase II for the Development of Anti-Dengue Therapeutics.Biotech (Basel (Switzerland)) · 2020Article
- AlphaSpace 2.0: Representing Concave Biomolecular Surfaces Using β-Clusters.Journal of chemical information and modeling · 2020Article
- Electrostatic-field and surface-shape similarity for virtual screening and pose prediction.Journal of computer-aided molecular design · 2019Article
- Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery.Frontiers in chemistry · 2018Review
- Pharmit: interactive exploration of chemical space.Nucleic acids research · 2016Article
- Modern approaches to accelerate discovery of new antischistosomal drugs.Expert opinion on drug discovery · 2016Review
- Fragment oriented molecular shapes.Journal of molecular graphics & modelling · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Shape-based virtual screening is an established and effective method for identifying small molecules that are similar in shape and function to a reference ligand. We describe a new method of shape-based virtual screening, volumetric aligned molecular shapes (VAMS). VAMS uses efficient data structures to encode and search molecular shapes. We demonstrate that VAMS is an effective method for shape-based virtual screening and that it can be successfully used as a prefilter to accelerate more computationally demanding search algorithms. Unique to VAMS is a novel minimum/maximum shape constraint query for precisely specifying the desired molecular shape. Shape constraint searches in VAMS are particularly efficient and millions of shapes can be searched in a fraction of a second. We compare the performance of VAMS with two other shape-based virtual screening algorithms a benchmark of 102 protein targets consisting of more than 32 million molecular shapes and find that VAMS provides a competitive trade-off between run-time performance and virtual screening performance.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.