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RNA-Puzzles Round V: blind predictions of 23 RNA structures.
Bu F, Adam Y, Adamiak RW, Antczak M, de Aquino BRH, Badepally NG, Batey RT, Baulin EF, Boinski P, Boniecki MJ, Bujnicki JM, Carpenter KA, Chacon J, Chen SJ, Chiu W, Cordero P, Das NK, Das R, Dawson WK, DiMaio F, Ding F, Dock-Bregeon AC, Dokholyan NV, Dror RO, Dunin-Horkawicz S, Eismann S, Ennifar E, Esmaeeli R, Farsani MA, Ferré-D'Amaré AR, Geniesse C, Ghanim GE, Guzman HV, Hood IV, Huang L, Jain DS, Jaryani F, Jin L, Joshi A, Karelina M, Kieft JS, Kladwang W, Kmiecik S, Koirala D, Kollmann M, Kretsch RC, Kurciński M, Li J, Li S, Magnus M, Masquida B, Moafinejad SN, Mondal A, Mukherjee S, Nguyen THD, Nikolaev G, Nithin C, Nye G, Pandaranadar Jeyeram IPN, Perez A, Pham P, Piccirilli JA, Pilla SP, Pluta R, Poblete S, Ponce-Salvatierra A, Popenda M, Popenda L, Pucci F, Rangan R, Ray A, Ren A, Sarzynska J, Sha CM, Stefaniak F, Su Z, Suddala KC, Szachniuk M, Townshend R, Trachman RJ 3rd, Wang J, Wang W, Watkins A, Wirecki TK, Xiao Y, Xiong P, Xiong Y, Yang J, Yesselman JD, Zhang J, Zhang Y, Zhang Z, Zhou Y, Zok T, Zhang D, Zhang S, Żyła A, Westhof E, Miao Z. Bu F, et al. Among authors: zhou y. Nat Methods. 2025 Feb;22(2):399-411. doi: 10.1038/s41592-024-02543-9. Epub 2024 Dec 2. Nat Methods. 2025. PMID: 39623050 Free PMC article.
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.
Miao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki J, Chen SJ, Cheng CY, Cheng Y, Chou FC, Das R, Dokholyan NV, Ding F, Geniesse C, Jiang Y, Joshi A, Krokhotin A, Magnus M, Mailhot O, Major F, Mann TH, Piątkowski P, Pluta R, Popenda M, Sarzynska J, Sun L, Szachniuk M, Tian S, Wang J, Wang J, Watkins AM, Wiedemann J, Xiao Y, Xu X, Yesselman JD, Zhang D, Zhang Y, Zhang Z, Zhao C, Zhao P, Zhou Y, Zok T, Żyła A, Ren A, Batey RT, Golden BL, Huang L, Lilley DM, Liu Y, Patel DJ, Westhof E. Miao Z, et al. Among authors: zhou y. RNA. 2020 Aug;26(8):982-995. doi: 10.1261/rna.075341.120. Epub 2020 May 5. RNA. 2020. PMID: 32371455 Free PMC article.
RLDOCK: A New Method for Predicting RNA-Ligand Interactions.
Sun LZ, Jiang Y, Zhou Y, Chen SJ. Sun LZ, et al. Among authors: zhou y. J Chem Theory Comput. 2020 Nov 10;16(11):7173-7183. doi: 10.1021/acs.jctc.0c00798. Epub 2020 Oct 23. J Chem Theory Comput. 2020. PMID: 33095555 Free PMC article.
An RNA aptamer that shifts the reduction potential of metabolic cofactors.
Samuelian JS, Gremminger TJ, Song Z, Poudyal RR, Li J, Zhou Y, Staller SA, Carballo JA, Roychowdhury-Saha M, Chen SJ, Burke DH, Heng X, Baum DA. Samuelian JS, et al. Among authors: zhou y. Nat Chem Biol. 2022 Nov;18(11):1263-1269. doi: 10.1038/s41589-022-01121-4. Epub 2022 Sep 12. Nat Chem Biol. 2022. PMID: 36097297 Free PMC article.
RNA-ligand molecular docking: advances and challenges.
Zhou Y, Jiang Y, Chen SJ. Zhou Y, et al. Wiley Interdiscip Rev Comput Mol Sci. 2022 May-Jun;12(3):e1571. doi: 10.1002/wcms.1571. Epub 2021 Aug 16. Wiley Interdiscip Rev Comput Mol Sci. 2022. PMID: 37293430 Free PMC article.
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