ArticleScientific reports2019
OptiPharm: An evolutionary algorithm to compare shape similarity.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- DeepDrugDiscovery identifies blood-brain barrier permeable autophagy enhancers for Alzheimer's disease.Nature biomedical engineering · 2026Article
- AutoDock-SS: AutoDock for Multiconformational Ligand-Based Virtual Screening.Journal of chemical information and modeling · 2024Article
- A two-layer mono-objective algorithm based on guided optimization to reduce the computational cost in virtual screening.Scientific reports · 2022Article
- 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
- Electrostatic-field and surface-shape similarity for virtual screening and pose prediction.Journal of computer-aided molecular design · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
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Abstract
Virtual Screening (VS) methods can drastically accelerate global drug discovery processes. Among the most widely used VS approaches, Shape Similarity Methods compare in detail the global shape of a query molecule against a large database of potential drug compounds. Even so, the databases are so enormously large that, in order to save time, the current VS methods are not exhaustive, but they are mainly local optimizers that can easily be entrapped in local optima. It means that they discard promising compounds or yield erroneous signals. In this work, we propose the use of efficient global optimization techniques, as a way to increase the quality of the provided solutions. In particular, we introduce OptiPharm, which is a parameterizable metaheuristic that improves prediction accuracy and offers greater computational performance than WEGA, a Gaussian-based shape similarity method. OptiPharm includes mechanisms to balance between exploration and exploitation to quickly identify regions in the search space with high-quality solutions and avoid wasting time in non-promising areas. OptiPharm is available upon request via email.
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Registered trials
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