ArticleNature communications2023
Automatic and accurate ligand structure determination guided by cryo-electron microscopy maps.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Structural and kinetic mechanisms of state-dependent potassium channel inhibition.Science advances · 2026Article
- Direct Detection and Atomic Modeling of Ligands in Cryo-EM Maps Using Deep Learning.bioRxiv : the preprint server for biology · 2026Article
- MarinePharmaceuticals (Basel, Switzerland) · 2026Article
- Cryo-electron microscopy reveals sequential binding and activation of Ryanodine Receptors by statin triplets.Nature communications · 2025Article
- Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics.PLoS computational biology · 2025Article
- Preparing for successful protein crystallization experiments.Acta crystallographica. Section F, Structural biology communications · 2025Article
- Target Engagement Assays in Early Drug Discovery.Journal of medicinal chemistry · 2025Review
- Article
- 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
- Structural insights into tecovirimat antiviral activity and poxvirus resistance.Nature microbiology · 2025Article
- Ligand and Residue Free Energy Perturbations Solve the Dual Binding Mode Proposal for an AThe journal of physical chemistry. B · 2025Article
- Ligand identification in CryoEM and X-ray maps using deep learning.Bioinformatics (Oxford, England) · 2024Article
- Ligand Identification in CryoEM and X-ray Maps Using Deep Learning.bioRxiv : the preprint server for biology · 2024Article
- The conserved HIV-1 spacer peptide 2 triggers matrix lattice maturation.bioRxiv : the preprint server for biology · 2024Article
- GOLEM: Automated and Robust Cryo-EM-Guided Ligand Docking with Explicit Water Molecules.Journal of chemical information and modeling · 2024Article
- AlphaFold2 structures guide prospective ligand discovery.Science (New York, N.Y.) · 2024Article
- Article
- ChemEM: Flexible Docking of Small Molecules in Cryo-EM Structures.Journal of medicinal chemistry · 2024Article
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Authors and funding
5 authors.
Funding
Abstract
Advances in cryo-electron microscopy (cryoEM) and deep-learning guided protein structure prediction have expedited structural studies of protein complexes. However, methods for accurately determining ligand conformations are lacking. In this manuscript, we develop EMERALD, a tool for automatically determining ligand structures guided by medium-resolution cryoEM density. We show this method is robust at predicting ligands along with surrounding side chains in maps as low as 4.5 Å local resolution. Combining this with a measure of placement confidence and running on all protein/ligand structures in the EMDB, we show that 57% of ligands replicate the deposited model, 16% confidently find alternate conformations, 22% have ambiguous density where multiple conformations might be present, and 5% are incorrectly placed. For five cases where our approach finds an alternate conformation with high confidence, high-resolution crystal structures validate our placement. EMERALD and the resulting analysis should prove critical in using cryoEM to solve protein-ligand complexes.
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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.