https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2025Muenks_EmeraldID2025Muenks EmeraldID - Revision history2026-05-24T21:06:50ZRevision history for this page on the wikiMediaWiki 1.44.2https://3demmethods.i2pc.es/index.php?title=2025Muenks_EmeraldID&diff=5087&oldid=prevWikiSysop: Created page with "== Citation == Muenks, A., Farrell, D.P., Zhou, G. and DiMaio, F. 2025. Automated identification of small molecules in cryoelectron microscopy data with density-and energy-guided evaluation. Structure. 33, 10 (2025), 1760–1770. == Abstract == Methodological improvements in cryoelectron microscopy (cryo-EM) have made it useful in ligandbound structure determination for biology and drug design. However, determining ligand conformation and identity is challenging at th..."2025-11-02T22:26:58Z<p>Created page with "== Citation == Muenks, A., Farrell, D.P., Zhou, G. and DiMaio, F. 2025. Automated identification of small molecules in cryoelectron microscopy data with density-and energy-guided evaluation. Structure. 33, 10 (2025), 1760–1770. == Abstract == Methodological improvements in cryoelectron microscopy (cryo-EM) have made it useful in ligandbound structure determination for biology and drug design. However, determining ligand conformation and identity is challenging at th..."</p>
<p><b>New page</b></p><div>== Citation ==<br />
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Muenks, A., Farrell, D.P., Zhou, G. and DiMaio, F. 2025. Automated identification of small molecules in cryoelectron microscopy data with density-and energy-guided evaluation. Structure. 33, 10 (2025), 1760–1770.<br />
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== Abstract ==<br />
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Methodological improvements in cryoelectron microscopy (cryo-EM) have made it useful in ligandbound<br />
structure determination for biology and drug design. However, determining ligand conformation<br />
and identity is challenging at the resolutions typical for cryo-EM. Automated methods can aid in ligand<br />
conformational modeling, but current ligand identification tools—developed for X-ray crystallography<br />
data—perform poorly at resolutions common for cryo-EM. Here, we present EMERALD-ID, a method<br />
capable of docking and evaluating small molecule conformations for ligand identification. EMERALDID<br />
identifies 44% of common ligands exactly and identifies closely related ligands in 66% of cases.<br />
We then use this tool to discover possible ligand identification errors, as well as previously<br />
unidentified ligands. Furthermore, we show EMERALD-ID identifying ligands from custom ligand<br />
libraries of various small molecule types, including human metabolites and drug fragments. Our method<br />
provides a valuable addition to cryo-EM modeling tools to improve small molecule model accuracy and<br />
quality.<br />
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== Keywords ==<br />
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== Links ==<br />
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https://www.cell.com/structure/fulltext/S0969-2126(25)00250-3<br />
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== Related software ==<br />
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== Related methods ==<br />
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== Comments ==</div>WikiSysop