ArticleJournal of medicinal chemistry2024
ChemEM: Flexible Docking of Small Molecules in Cryo-EM Structures.
Article in Journal of medicinal chemistry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- The Batten disease protein CLN8 is a stereospecific acyltransferase in bis(monoacylglycero)phosphate biosynthesis.Nature cell biology · 2026Article
- Ion Channel-Targeting Modulators in Glioma: Pharmacological Advances and Therapeutic Perspectives.International journal of molecular sciences · 2026Review
- Short Cationic ACTH-Related Peptides Can Modulate the NaInternational journal of molecular sciences · 2026Article
- Cooperative mechanism of neurotransmitter recognition and transport by the human vesicular polyamine transporter.Nature communications · 2026Article
- Direct Detection and Atomic Modeling of Ligands in Cryo-EM Maps Using Deep Learning.bioRxiv : the preprint server for biology · 2026Article
- Reading between the Chains: Surface Mapping and Druggable Pockets on the Biological Assemblies of DENV-2's Protein E.ACS omega · 2026Article
- Developments and challenges in hit progression within fragment-based drug discovery.Nature communications · 2026Review
- Combining Cryo-EM with Computational Approaches To Revolutionize Structural Biology.The protein journal · 2025Review
- Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics.PLoS computational biology · 2025Article
- Overcoming translational barriers in RNA-protein docking: enhancing computational accuracy for targeted drug discovery.Future medicinal chemistry · 2025Review
- Structure and mechanism of human vesicular polyamine transporter.Nature communications · 2025Article
- Molecular basis of pyruvate transport and inhibition of the human mitochondrial pyruvate carrier.Science advances · 2025Article
- The physics-AI dialogue in drug design.RSC medicinal chemistry · 2025Review
- 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
- EMICSS: added-value annotations for EMDB entries.Bioinformatics advances · 2025Article
- Structural bases for NaNature communications · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Cryo-electron microscopy (cryo-EM), through resolution advancements, has become pivotal in structure-based drug discovery. However, most cryo-EM structures are solved at 3-4 Å resolution, posing challenges for small-molecule docking and structure-based virtual screening due to issues in the precise positioning of ligands and the surrounding side chains. We present ChemEM, a software package that employs cryo-EM data for the accurate docking of one or multiple ligands in a protein-binding site. Validated against a highly curated benchmark of high- and medium-resolution cryo-EM structures and the corresponding high-resolution controls, ChemEM displayed impressive performance, accurately placing ligands in all but one case, often surpassing cryo-EM PDB-deposited solutions. Even without including the cryo-EM density, the ChemEM scoring function outperformed the well-established AutoDock Vina score. Using ChemEM, we illustrate that valuable information can be extracted from maps at medium resolution and underline the utility of cryo-EM structures for drug discovery.
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Registered trials
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