ReviewFrontiers in chemistry2018
Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery.
Review in Frontiers in chemistry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers, 1 of them a synthesis that pooled it.
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Who cites it
78 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Insights into the computer-aided drug design and discovery based on anthraquinone scaffold for cancer treatment: A systematic review.PloS one · 2024Pooled it
- The emerging synergy of experimental and computational approaches for therapeutic modulation of biomolecular condensates.SLAS discovery : advancing life sciences R & D · 2026Review
- 1,5-Disubstituted Tetrazoles as Promising Anticancer Resistance Agents: A Chemoinformatic Characterization.ACS omega · 2026Article
- A chemoinformatics-guided platform for efficient discovery of RNA-binding small molecules: Proof-of-concept for myotonic dystrophy type 1.bioRxiv : the preprint server for biology · 2026Article
- Natural Products in Epilepsy Treatment: From Traditional Medicine Towards Computational Drug Discovery.Current issues in molecular biology · 2026Review
- ComTarget: Small-Molecule Target Prediction with Combinatorial Modeling.Pharmaceuticals (Basel, Switzerland) · 2026Article
- In-silico assessment of phytochemical derivatives generated using CHEESE webserver for advancement of druggable candidate in pancreatic cancer therapy.In silico pharmacology · 2026Article
- LiraSearch-ultrafast ligand shape and electrostatic matching server.Bioinformatics advances · 2026Article
- A multi-stage computational pipeline for repurposing FDA-approved drugs: application to EGFR C797S-mutant NSCLC.Frontiers in chemistry · 2026Article
- Scaffold Hopping and Optimization of Thiazole Hybrids as Selective PIN1 Inhibitors: A Computational Study.Medicinal chemistry (Shariqah (United Arab Emirates)) · 2026Article
- SGEDiff: a subgraph-enriched diffusion model for structure-based 3D molecular generation.Journal of cheminformatics · 2025Article
- The covalent docking software landscape: features and applications in drug design.Briefings in bioinformatics · 2025Review
- Integration of diverse bioactivity data into the Chemical Checker compound universe.Nature protocols · 2025Review
- Scaffold Hopping in Tuberculosis Drug Discovery: Principles, Applications, and Case Studies.Journal of medicinal chemistry · 2025Review
- Identification of Potential Pteridin Reductase-1 Inhibitors for the Treatment of Leishmaniasis: A Bioinformatics Approach.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Recent advances in molecular representation methods and their applications in scaffold hopping.npj drug discovery · 2025Review
- Structure-Based Discovery of Orthosteric Non-Peptide GLP-1R Agonists via Integrated Virtual Screening and Molecular Dynamics.International journal of molecular sciences · 2025Article
- Hypershape Recognition: A General Framework for Moment-Based Molecular Similarity.Journal of chemical information and modeling · 2025Article
- Integrative Analysis of Drug Co-Prescriptions in Peritoneal Dialysis Reveals Molecular Targets and Novel Strategies for Intervention.Journal of clinical medicine · 2025Article
- StructureNet: Physics-Informed Hybridized Deep Learning Framework for Protein-Ligand Binding Affinity Prediction.Bioengineering (Basel, Switzerland) · 2025Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular similarity is a key concept in drug discovery. It is based on the assumption that structurally similar molecules frequently have similar properties. Assessment of similarity between small molecules has been highly effective in the discovery and development of various drugs. Especially, two-dimensional (2D) similarity approaches have been quite popular due to their simplicity, accuracy and efficiency. Recently, the focus has been shifted toward the development of methods involving the representation and comparison of three-dimensional (3D) conformation of small molecules. Among the 3D similarity methods, evaluation of shape similarity is now gaining attention for its application not only in virtual screening but also in molecular target prediction, drug repurposing and scaffold hopping. A wide range of methods have been developed to describe molecular shape and to determine the shape similarity between small molecules. The most widely used methods include atom distance-based methods, surface-based approaches such as spherical harmonics and 3D Zernike descriptors, atom-centered Gaussian overlay based representations. Several of these methods demonstrated excellent virtual screening performance not only retrospectively but also prospectively. In addition to methods assessing the similarity between small molecules, shape similarity approaches have been developed to compare shapes of protein structures and binding pockets. Additionally, shape comparisons between atomic models and 3D density maps allowed the fitting of atomic models into cryo-electron microscopy maps. This review aims to summarize the methodological advances in shape similarity assessment highlighting advantages, disadvantages and their application in drug discovery.
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