ArticleStructure (London, England : 1993)2020
GemSpot: A Pipeline for Robust Modeling of Ligands into Cryo-EM Maps.
Article in Structure (London, England : 1993), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- Structure-based design of subtype-selective psychedelic analogs.Nature communications · 2026Article
- Structural basis of opioid receptor activation by PCP and ketamine.Nature structural & molecular biology · 2026Article
- The structure of the dopamine DScience advances · 2026Article
- Direct Detection and Atomic Modeling of Ligands in Cryo-EM Maps Using Deep Learning.bioRxiv : the preprint server for biology · 2026Article
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- Structural insights into coffee bitter taste perception by TAS2R43 receptor.Nature structural & molecular biology · 2026Article
- Variable Resolution Maps (VRM) in CCTBX and Phenix: Accounting For Local Resolution In cryoEM.bioRxiv : the preprint server for biology · 2026Article
- Designing Rigid Protein Fiducials to Visualize GPCR Conformational States.bioRxiv : the preprint server for biology · 2026Article
- Structural basis of specific lysine transport by Pseudomonas aeruginosa permease LysP.Nature communications · 2025Article
- UDP-glucose and MRS2905 agonist-bound states of the purinergic P2YCommunications biology · 2025Article
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- Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics.PLoS computational biology · 2025Article
- Structural basis of stepwise proton sensing-mediated GPCR activation.Cell research · 2025Article
- The structural diversity of psychedelic drug actions revealed.Nature communications · 2025Article
- Structure-guided design of partial agonists at an opioid receptor.Nature communications · 2025Article
- DockEM: an enhanced method for atomic-scale protein-ligand docking refinement leveraging low-to-medium resolution cryo-EM density maps.Briefings in bioinformatics · 2025Article
- Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance.Protein science : a publication of the Protein Society · 2025Article
- Rational Identification of Ritonavir as IL-20 Receptor A Ligand Endowed with Antiproliferative Properties in Breast Cancer Cells.International journal of molecular sciences · 2025Article
- Structure- and Ligand-Based Virtual Screening for Identification of Novel TRPV4 Antagonists.Molecules (Basel, Switzerland) · 2024Article
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4 authors.
Funding
Abstract
Producing an accurate atomic model of biomolecule-ligand interactions from maps generated by cryoelectron microscopy (cryo-EM) often presents challenges inherent to the methodology and the dynamic nature of ligand binding. Here, we present GemSpot, an automated pipeline of computational chemistry methods that take into account EM map potentials, quantum mechanics energy calculations, and water molecule site prediction to generate candidate poses and provide a measure of the degree of confidence. The pipeline is validated through several published cryo-EM structures of complexes in different resolution ranges and various types of ligands. In all cases, at least one identified pose produced both excellent interactions with the target and agreement with the map. GemSpot will be valuable for the robust identification of ligand poses and drug discovery efforts through cryo-EM.
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