https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2026Jain_ProtAcid 2026-08-24T22:15:48Z Revision history for this page on the wiki MediaWiki 1.44.2 https://3demmethods.i2pc.es/index.php?title=2026Jain_ProtAcid&diff=5271&oldid=prev 2026-08-24T05:12:03Z

<p>Created page with &quot;== Citation == Jain, A., Cao, K. and Kihara, D. 2026. Computational approaches for protein–DNA/RNA complex modeling for Cryo-EM maps. Current Protocols. 6, 8 (2026), e70409. == Abstract == Cryogenic electron microscopy (cryo-EM) has become a key method in structural biology for determining macromolecular structures. Numerous computational tools have been developed to build atomic models from cryo-EM density maps. However, relatively few tools are available for model...&quot;</p> <p><b>New page</b></p><div>== Citation ==<br /> <br /> Jain, A., Cao, K. and Kihara, D. 2026. Computational approaches for protein–DNA/RNA complex modeling for Cryo-EM maps. Current Protocols. 6, 8 (2026), e70409.<br /> <br /> == Abstract ==<br /> <br /> Cryogenic electron microscopy (cryo-EM) has become a key method in structural<br /> biology for determining macromolecular structures. Numerous computational<br /> tools have been developed to build atomic models from cryo-EM density<br /> maps. However, relatively few tools are available for modeling protein–<br /> nucleic acid complexes. Here, we describe how to use two such methods developed<br /> by our group, ComplexModeler and CryoZeta, with a focus on modeling<br /> protein–nucleic acid complexes. Both tools are available through the EMSuite<br /> web server, a freely accessible platform that hosts multiple methods for<br /> cryo-EM structure modeling and validation. ComplexModeler integrates Diff-<br /> Modeler and CryoREAD to construct protein–DNA/RNA complex structures<br /> at resolutions of up to 5 Å. DiffModeler employs a diffusion model for backbone<br /> tracing, followed by fitting AlphaFold2-predicted protein structures into<br /> the traced backbone. CryoREAD identifies nucleotide components (phosphate,<br /> sugar, and base), constructs the backbone, assigns sequences, and builds full<br /> atomic models of DNA/RNA chains. CryoZeta uses a diffusion-based generative<br /> model that integrates sequence-based structure prediction with cryo-EM<br /> density features to generate accuratemodels of proteins, nucleic acids, and their<br /> complexes. This article describes how to use these two tools on the EMSuite<br /> web server through two modeling examples.<br /> <br /> == Keywords ==<br /> <br /> == Links ==<br /> <br /> https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.70409<br /> <br /> == Related software ==<br /> <br /> == Related methods ==<br /> <br /> == Comments ==</div>

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