Publication The Nucleic Acids Circular Dichroism and Fourier Transform Databases NACDDB and NAIRDB: New Tools for RNA Structural Analysis. Mosca K, Balduzzi E, Sordyl D, Cappannini A, Geinguenaud F, Wien F, Arluison V, Bujnicki JM. Methods Mol Biol. 2026 Publication MODOMICS: a database of RNA modifications and related information. 2025 update and 20th anniversary Sordyl D, Boileau E, Bernat A, Maiti S, Mukherjee S, Moafinejad SN, Farsani MA, Shavina A, Cappannini A, Agostini G, Conticello SG, Stefaniak F, Dieterich C, Purta E, Bujnicki JM. Nucleic Acids Res. 2026 Publication Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16.65 Kretsch RC, Posani E, Baulin EF, Bujnicki JM, Bussi G, Cheatham TE 3rd, Chen SJ, Elofsson A, Farsani MA, Fisher ON, Gromiha MM, Gupta A, Hamada M, Harini K, Hu G, Huang D, Iwakiri J, Jain A, Kagaya Y, Kihara D, Kmiecik S, Krishnan SR, Kurisaki I, Languin-Cattoën O, Li J, Li S, Malekzadeh K, Nakamura T, Ni W, Nithin C, Palo MZ, Park JH, Pilla SP, Poblete S, Pucci F, Punuru P, Saha A, Sato K, Srivastava A, Terashi G, Tugolukova E, Verburgt J, Wuyun Q, Zerze GH, Zhang K, Zhang S, Zheng W, Zhou Y, Chiu W, Case DA, Das R. Proteins. 2026 Publication Evaluation of single-template ligand-based methods for the discovery of small-molecule nucleic acid binders. Bajusz D, Rácz A, Bujnicki JM, Stefaniak F. Brief Bioinform. 2025 Publication Exploring GNRA tetraloop-like motifs in nucleic acid 3D structures. Bujnicki JM, Baulin EF. Sci Rep. 2025 Publication Translon: a single term for translated regions. Świrski MI et al (with Bujnicki JM) Nat Methods. 2025 Publication Modeling flexible RNA 3D structures and RNA-protein complexes. Loureiro RJ, Maiti S, Mondal K, Mukherjee S, Bujnicki JM. Curr Opin Struct Biol. 2025 Publication ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations. Baulin EF, Bohdan DR, Kowalski D, Serwatka M, Świerczyńska J, Żyra Z, Bujnicki JM. Genome Biol. 2025 Publication Structure of fungal tRNA ligase Trl1 with RNA reveals conserved substrate-binding principles. Köhler S, Kopp J, Maiti S, Bujnicki JM, Peschek J. Nat Struct Mol Biol. 2025 Publication Determining the effects of pseudouridine incorporation on human tRNAs. Biela AD, Nowak JS, Biela AP, Mukherjee S, Moafinejad SN, Maiti S, Chramiec-Głąbik A, Mehta R, Jeżowski J, Dobosz D, Dahate P, Arluison V, Wien F, Indyka P, Rawski M, Bujnicki JM, Lin TY, Glatt S. EMBO J. 2025 Publication Protein-RNA Docking Benchmark v3.0 Integrated With Binding Affinity. Kant S, Nithin C, Mukherjee S, Maity A, Bahadur RP. Proteins. 2025 Publication DesiRNA: structure-based design of RNA sequences with a replica exchange Monte Carlo approach. Wirecki TK, Lach G, Badepally NG, Moafinejad SN, Jaryani F, Klaudel G, Nec K, Baulin EF, Bujnicki JM. Nucleic Acids Res. 2025 Publication 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. Nat Methods. 2025 Publication Sci-ModoM: a quantitative database of transcriptome-wide high-throughput RNA modification sites. Boileau E, Wilhelmi H, Busch A, Cappannini A, Hildebrand A, Bujnicki JM, Dieterich C. Nucleic Acids Res . 2025 Publication NAIRDB: a database of Fourier transform infrared (FTIR) data for nucleic acids. Balduzzi E, Geinguenaud F, Sordyl D, Maiti S, Farsani MA, Nikolaev G, Arluison V, Bujnicki JM. Nucleic Acids Res. 2025 Publication Role of Non-Canonical Stacking Interactions of Heterocyclic RNA Bases in Ribosome Function. Metelev VG, Baulin EF, Bogdanov AA. Biochemistry (Mosc). 2024 Publication Cryo-EM structure of raiA ncRNA from Clostridium reveals a new RNA 3D fold. Goud Badepally N, Rocha de Moura T, Purta E, Baulin EF, Bujnicki JM. J Mol Biol. 2024 Publication The three YTHDF paralogs and VIRMA are strong cross-histotype tumor driver candidates among m6A core genes. Destefanis E, Sighel D, Dalfovo D, Gilmozzi R, Broso F, Cappannini A, Bujnicki JM, Romanel A, Dassi E, Quattrone A. NAR Cancer. 2024 Publication Advances in the field of RNA 3D structure prediction and modeling, with purely theoretical approaches, and with the use of experimental data. Mukherjee S, Moafinejad SN, Badepally NG, Merdas K, Bujnicki JM. Structure. 2024 Publication Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens. Perlinska AP, Nguyen ML, Pilla SP, Staszor E, Lewandowska I, Bernat A, Purta E, Augustyniak R, Bujnicki JM, Sulkowska JI. Front Mol Biosci. 2024 Publication 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, Jeyeram IPNP, Nikolaev G, Magnus M, Farsani MA, Badepally NG, Wirecki TK, Stefaniak F, Bujnicki JM. Nucleic Acids Res. 2024 Publication ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment. Bohdan DR, Bujnicki JM, Baulin EF. Nucleic Acids Res. 2024 Publication Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes. de Moura TR, Purta E, Bernat A, Martín-Cuevas EM, Kurkowska M, Baulin EF, Mukherjee S, Nowak J, Biela AP, Rawski M, Glatt S, Moreno-Herrero F, Bujnicki JM. Nucleic Acids Res. 2024 Publication Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology. Niemyska W, Mukherjee S, Gren BA, Niewieczerzal S, Bujnicki JM, Sulkowska JI. J Mol Biol.. 2024 Publication MODOMICS: a database of RNA modifications and related information. 2023 update. Cappannini A, Ray A, Purta E, Mukherjee S, Boccaletto P, Moafinejad SN, Lechner A, Barchet C, Klaholz BP, Stefaniak F, Bujnicki JM. Nucleic Acids Res. . 2024 Publication DEGRONOPEDIA: a web server for proteome-wide inspection of degrons. Szulc NA, Stefaniak F, Piechota M, Soszyńska A, Piórkowska G, Cappannini A, Bujnicki JM, Maniaci C, Pokrzywa W. Nucleic Acids Res. 2024 Preprint DesiRNA: structure-based design of RNA sequences with a Monte Carlo approach. Wirecki T, Lach G, Jaryani F, Badepally NG, Moafinejad SN, Klaudel G, Bujnicki JM. bioRxiv. 2023 Preprint SQUARNA - an RNA secondary structure prediction method based on a greedy stem formation model. Bohdan DR, Nikolaev GI, Bujnicki JM, Baulin EF bioRxiv. 2023 Publication RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints. Baulin EF, Mukherjee S, Moafinejad SN, Wirecki TK, Badepally NG, Jaryani F, Stefaniak F, Amiri Farsani M, Ray A, Rocha de Moura T, Bujnicki JM. Proteins. 2023 Publication RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints. Chojnowski G, Zaborowski R, Magnus M, Mukherjee S, Bujnicki JM. Bioinformatics. 2023