Publication RNA target highlights in CASP15: Evaluation of predicted models by structure providers. Kretsch RC, Andersen ES, Bujnicki JM, Chiu W, Das R, Luo B, Masquida B, McRae EKS, Schroeder GM, Su Z, Wedekind JE, Xu L, Zhang K, Zheludev IN, Moult J, Kryshtafovych A. Proteins. 2023 Publication Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing. Luo BN et al. with Bujnicki JM. Nature Catalysis. 2023 Publication A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures. Bohdan DR, Voronina VV, Bujnicki JM, Baulin EF. Nucleic Acids Res.. 2023 Publication Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to RNA. Szulc NA, Mackiewicz Z, Bujnicki JM, Stefaniak F. Brief Bioinform.. 2023 Publication Structural basis of sRNA RsmZ regulation of Pseudomonas aeruginosa virulence. Jia X, Pan Z, Yuan Y, Luo B, Luo Y, Mukherjee S, Jia G, Liu L, Ling X, Yang X, Miao Z, Wei X, Bujnicki JM, Zhao K, Su Z. Cell Res.. 2023 Publication NACDDB: Nucleic Acid Circular Dichroism Database. Cappannini A, Mosca K, Mukherjee S, Moafinejad SN, Sinden RR, Arluison V, Bujnicki J, Wien F. Nucleic Acids Res.. 2023 Publication 1D2DSimScore: A novel method for comparing contacts in biomacromolecules and their complexes. Moafinejad SN, Pandaranadar Jeyeram IPN, Jaryani F, Shirvanizadeh N, Baulin EF, Bujnicki JM. Protein Sci.. 2023 Publication Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field. Sieradzan AK, Czaplewski C, Krupa P, Mozolewska MA, Karczyńska AS, Lipska AG, Lubecka EA, Gołaś E, Wirecki T, Makowski M, Ołdziej S, Liwo A. Methods Mol Biol. 2022 Publication Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models. Gumna J, Antczak M, Adamiak RW, Bujnicki JM, Chen SJ, Ding F, Ghosh P, Li J, Mukherjee S, Nithin C, Pachulska-Wieczorek K, Ponce-Salvatierra A, Popenda M, Sarzynska J, Wirecki T, Zhang D, Zhang S, Zok T, Westhof E, Miao Z, Szachniuk M, Rybarczyk A. Int J Mol Sci. 2022 Publication fingeRNAt-A novel tool for high-throughput analysis of nucleic acid-ligand interactions. Szulc NA, Mackiewicz Z, Bujnicki JM, Stefaniak F. PLoS Comput Biol.. 2022 Publication Molecular insights into RNA recognition and gene regulation by the TRIM-NHL protein Mei-P26. Salerno-Kochan A, Horn A, Ghosh P, Nithin C, Kościelniak A, Meindl A, Strauss D, Krutyhołowa R, Rossbach O, Bujnicki JM, Gaik M, Medenbach J, Glatt S. Life Sci Alliance. 2022 Publication DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes. Mohammadi-Arani R, Javadi-Zarnaghi F, Boccaletto P, Bujnicki JM, Ponce-Salvatierra A. Nucleic Acids Res. 2022 Publication MODOMICS: a database of RNA modification pathways. 2021 update. Boccaletto P, Stefaniak F, Ray A, Cappannini A, Mukherjee S, Purta E, Kurkowska M, Shirvanizadeh N, Destefanis E, Groza P, Avşar G, Romitelli A, Pir P, Dassi E, Conticello SG, Aguilo F, Bujnicki JM. Nucleic Acids Res. 2022 Constrained peptides mimic a viral suppressor of RNA silencing. Kuepper A, McLoughlin NM, Neubacher S, Yeste-Vázquez A, Collado Camps E, Nithin C, Mukherjee S, Bethge L, Bujnicki JM, Brock R, Heinrichs S, Grossmann TN. Nucleic Acids Res. . 2021 Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA. Wegrzyn K, Zabrocka E, Bury K, Tomiczek B, Wieczor M, Czub J, Uciechowska U, Moreno-Del Alamo M, Walkow U, Grochowina I, Dutkiewicz R, Bujnicki JM, Giraldo R, Konieczny I. Nucleic Acids Res.. 2021 AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses. Stefaniak F, Bujnicki JM. PLoS Comput Biol.. 2021 RNA and DNA G-quadruplexes bind to human dicer and inhibit its activity. Koralewska N, Szczepanska A, Ciechanowska K, Wojnicka M, Pokornowska M, Milewski MC, Gudanis D, Baranowski D, Nithin C, Bujnicki JM, Gdaniec Z, Figlerowicz M, Kurzynska-Kokorniak A. Cell Mol Life Sci.. 2021 DNAmoreDB, a database of DNAzymes. Ponce-Salvatierra A, Boccaletto P, Bujnicki JM. Nucleic Acids Res.. 2021 Publication Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements. Manfredonia I, Nithin C, Ponce-Salvatierra A, Ghosh P, Wirecki TK, Marinus T, Ogando NS, Snijder EJ, van Hemert MJ, Bujnicki JM, Incarnato D. Nucleic Acids Res. 2020 Luciferase reporter assay for small-molecule inhibitors of MIR92b-3p function: Screening cyanopeptolins produced by Nostoc from the Baltic Sea. Brzuzan P, Mazur-Marzec H, Florczyk M, Stefaniak F, Fidor A, Konkel R, Woźny M. Toxicol In Vitro.. 2020 Benzoxazepine-Derived Selective, Orally Bioavailable Inhibitor of Human Acidic Mammalian Chitinase. Andryianau G, Kowalski M, Piotrowicz MC, Rajkiewicz AA, Dymek B, Sklepkiewicz PL, Pluta E, Stefaniak F, Czestkowski W, Olejniczak S, Mazur M, Niedziejko P, Koralewski R, Matyszewski K, Gruza M, Zagozdzon A, Salamon M, Rymaszewska A, Welzer M, Dzwonek K, Golab J, Olczak J, Bartoszewicz A, Golebiowski A. ACS Med Chem Lett.. 2020 RNAProbe: a web server for normalization and analysis of RNA structure probing data. Wirecki TK, Merdas K, Bernat A, Boniecki MJ, Bujnicki JM, Stefaniak F. Nucleic Acids Res. . 2020 RNA-Puzzles Round IV: 3D Structure Predictions of Four Ribozymes and Two Aptamers. Miao Z et al. (Boniecki MJ, Bujnicki JM, Joshi A, Magnus M, Piatkowski P, Pluta R.) RNA. 2020 Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition. Lambert AR, Hallinan JP, Werther R, Głów D, Stoddard BL. Structure. 2020 RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools. Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM, Westhof E, Szachniuk M, Miao Z. Nucleic Acids Res.. 2020 A combined structural and biochemical approach reveals translocation and stalling of UvrB on the DNA lesion as a mechanism of damage verification in bacterial nucleotide excision repair. Jaciuk M, Swuec P, Gaur V, Kasprzak JM, Renault L, Dobrychłop M, Nirwal S, Bujnicki JM, Costa A, Nowotny M. DNA Repair (Amst).. 2020 Development of Dual Chitinase Inhibitors as Potential New Treatment for Respiratory System Diseases. Mazur M, Dymek B, Koralewski R, Sklepkiewicz P, Olejniczak S, Mazurkiewicz M, Piotrowicz M, Salamon M, Jędrzejczak K, Zagozdzon A, Czestkowski W, Matyszewski K, Borek B, Bartoszewicz A, Pluta E, Rymaszewska A, Mozga W, Stefaniak F, Dobrzański P, Dzwonek K, Golab J, Golebiowski A, Olczak J. J Med Chem. . 2019 Improving selectivity of DNA-RNA binding zinc finger using directed evolution. Sulej AA BMC Res Notes. . 2019 RRMdb – an evolutionary-oriented database of RNA recognition motif sequences. Nowacka M, Boccaletto P, Jankowska E, Jarzynka T, Bujnicki JM, Dunin-Horkawicz S. Database. 2019 Matching tRNA modifications in humans to their known and predicted enzymes. de Crecy-Lagard V, Boccaletto P, Mangleburg C, Sharma P, Lowe T, Leidel S, Bujnicki JM. Nucleic Acids Res.. 2019