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Page 1
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: de aquino brh. 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.
SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories.
Moafinejad SN, de Aquino BRH, Boniecki MJ, Pandaranadar Jeyeram IPN, Nikolaev G, Magnus M, Farsani MA, Badepally NG, Wirecki TK, Stefaniak F, Bujnicki JM. Moafinejad SN, et al. Among authors: de aquino brh. Nucleic Acids Res. 2024 Jul 5;52(W1):W368-W373. doi: 10.1093/nar/gkae356. Nucleic Acids Res. 2024. PMID: 38738621 Free PMC article.
Ionized water confined in graphene nanochannels.
de Aquino BRH , Ghorbanfekr-Kalashami H , Neek-Amal M , Peeters FM . de Aquino BRH , et al. Phys Chem Chem Phys. 2019 May 8;21(18):9285-9295. doi: 10.1039/c9cp00075e. Phys Chem Chem Phys. 2019. PMID: 30931451