View source for 9yx9


==SARS-CoV-2 SL5 rotated junction==
<StructureSection load='9yx9' size='340' side='right'caption='[[9yx9]], [[Resolution|resolution]] 6.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9yx9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9YX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9YX9 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 6.5&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9yx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9yx9 OCA], [https://pdbe.org/9yx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9yx9 RCSB], [https://www.ebi.ac.uk/pdbsum/9yx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9yx9 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Consistently accurate 3D nucleic acid structure prediction would facilitate studies of the diverse RNA and DNA molecules underlying life. In CASP16, blind predictions for 42 targets canvassing a full array of nucleic acid functions, from dopamine binding by DNA to formation of elaborate RNA nanocages, were submitted by 65 groups from 46 different labs worldwide. In contrast to concurrent protein structure predictions, performance on nucleic acids was generally poor, with no predictions of previously unseen natural RNA structures achieving TM-scores above 0.8. Even though automated server performance has improved, all top-performing groups were human expert predictors: Vfold, GuangzhouRNA-human, and KiharaLab. Good performance on one template-free modeling target (OLE RNA) and accurate global secondary structure prediction suggested that structural information can be extracted from multiple sequence alignments. However, 3D accuracy generally appeared to depend on the availability of closely related 3D structure templates, and predictions still did not achieve consistent recovery of pseudoknots, singlet Watson-Crick-Franklin pairs, non-canonical pairs, or tertiary motifs like A-minor interactions. For the first time, blind predictions of nucleic acid interactions with small molecules, proteins, and other nucleic acids could be assessed in CASP16. As with nucleic acid monomers, prediction accuracy for nucleic acid complexes was generally poor unless 3D templates were available. Accounting for template availability, there has not been a notable increase in nucleic acid modeling accuracy between previous blind challenges and CASP16.

Assessment of Nucleic Acid Structure Prediction in CASP16.,Kretsch RC, Hummer AM, He S, Yuan R, Zhang J, Karagianes T, Cong Q, Kryshtafovych A, Das R Proteins. 2026 Jan;94(1):192-217. doi: 10.1002/prot.70072. Epub 2025 Oct 30. PMID:41165252<ref>PMID:41165252</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 9yx9" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Severe acute respiratory syndrome coronavirus 2]]
[[Category: Chiu W]]
[[Category: Das R]]
[[Category: Kretsch RC]]
[[Category: Xu L]]