Virtual screening strategies in drug design - methods and applications Bielska E, Lucas X, Czerwoniec A, Kasprzak JM, Kaminska KH, Bujnicki JM BioTechnologia. 2011 STAT1 as a novel therapeutical target in pro-atherogenic signal integration of IFNg, TLR4 and IL-6 in vascular disease Sikorski K, Czerwoniec A, Bujnicki JM, Wesoly J, Bluyssen HAR Cytokine Growth Factor Rev.. 2011 RNA tertiary structure prediction with ModeRNA Rother M, Rother K, Puton T, Bujnicki JM Brief Bioinform. 2011 Databases and bioinformatics tools for the study of DNA repair Milanowska K, Rother K, Bujnicki JM Mol Biol Int. 2011 Effect of substrate features and mutagenesis of active site tyrosine residues on the reaction course catalysed by Trypanosoma brucei sterol C-24-methyltransferase Liu J, Ganapathy K, Wywial E, Bujnicki JM, Nwogwugwu CA, Nes WD Biochem J. 2011 Identification and modeling of a phosphatase-like domain in a tRNA 2'-O-ribosyl phosphate transferase Rit1p Czerwoniec A, Bujnicki JM Cell Cycle. 2011 RNAcentral: A vision for an international database of RNA sequences Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C RNA. 2011 ModeRNA: a tool for comparative modeling of RNA 3D structure Rother M, Rother K, Puton T, Bujnicki JM Nucleic Acids Res. 2011 2'-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family Werner M, Purta E, Kaminska KH, Cymerman IA, Campbell DA, Mittra B, Zamudio JR, Sturm NR, Jaworski J, Bujnicki JM Nucleic Acids Res. 2011 DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking Tuszynska I, Bujnicki JM BMC Bioinformatics. 2011 ModeRNA server: an online tool for modeling RNA 3D structures Rother M, Milanowska K, Puton T, Jeleniewicz J, Rother K, Bujnicki JM Bioinformatics. 2011 RNA and protein 3D structure modeling: similarities and differences Rother K, Rother M, Boniecki M, Puton T, Bujnicki JM J Mol Model.. 2011 A single zinc ion is sufficient for an active Trypanosoma brucei tRNA editing deaminase Spears JL, Rubio MA, Gaston KW, Wywial E, Strikoudis A, Bujnicki JM, Papavasiliou FN, Alfonzo JD J Biol Chem. 2011 Evidence for an evolutionary antagonism between Mrr and Type III modification systems. Tesfazgi Mebrhatu M, Wywial E, Ghosh A, Michiels CW, Lindner AB, Taddei F, Bujnicki JM, Van Melderen L, Aertsen A Nucleic Acids Res. 2011 Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit Husain N, Obranic S, Koscinski L, Seetharaman J, Babic F, Bujnicki JM, Maravic-Vlahovicek G, Sivaraman J Nucleic Acids Res. 2011 "4D Biology for health and disease" workshop report Abrahams JP, Apweiler R, Balling R, Bertero MG, Bujnicki JM, Chayen NE, Chène P, Corthals GL, Dyląg T, Förster F, Heck AJ, Henderson PJ, Herwig R, Jehenson P, Kokalj SJ, Laue E, Legrain P, Martens L, Migliorini C, Musacchio A, Podobnik M, Schertler GF, Sc N Biotechnol. 2011 REPAIRtoire-a database of DNA repair pathways Milanowska K, Krwawicz J, Papaj G, Kosinski J, Poleszak K, Lesiak J, Osinska E, Rother K, Bujnicki JM Nucleic Acids Res. 2011 BioCatalogue: a universal catalogue of web services for the life sciences Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA Nucleic Acids Res. 2010 Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site Tkaczuk KL J Mol Model.. 2010 IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities Rother K, Hoffmann S, Bulik S, Hoppe A, Gasteiger J, Holzhütter HG Biophys J.. 2010 A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI). Khan F, Furuta Y, Kawai M, Kaminska KH, Ishikawa K, Bujnicki JM, Kobayashi I Nucleic Acids Res. 2010 Predicting atomic details of the unfolding pathway for YibK, a knotted protein from the SPOUT superfamily Tuszynska I, Bujnicki JM J Biomol Struct Dyn. 2010 Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria. Kaminska KH, Purta E, Hansen LH, Bujnicki JM, Vester B, Long KS Nucleic Acids Res. 2010 The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket. Zhou X, Chua TK, Tkaczuk KL, Bujnicki JM, Sivaraman J J Struct Biol. 2010 Physiological truncation and domain organization of a novel uracil-DNA-degrading factor. Pukáncsik M, Békési A, Klement E, Hunyadi-Gulyás E, Medzihradszky KF, Kosinski J, Bujnicki JM, Alfonso C, Rivas G, Vértessy BG FEBS J. 2010 The YTH domain is a novel RNA binding domain. Zhang Z, Theler D, Kaminska KH, Hiller M, de la Grange P, Pudimat R, Rafalska I, Heinrich B, Bujnicki JM, Allain FH, Stamm S J Biol Chem. 2010 Co-evolution-driven switch of J-protein specificity towards an Hsp70 partner. Pukszta S, Schilke B, Dutkiewicz R, Kominek J, Moczulska K, Stepien B, Reitenga KG, Bujnicki JM, Williams B, Craig EA, Marszalek J EMBO Rep. 2010 New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA. Kempenaers M, Roovers M, Oudjama Y, Tkaczuk KL, Bujnicki JM, Droogmans L Nucleic Acids Res. 2010 Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m7G methyltransferases. Husain N, Tkaczuk KL, Tulsidas SR, Kaminska KH, Cubrilo S, Maravić-Vlahovicek G, Bujnicki JM, Sivaraman J Nucleic Acids Res. 2010 Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair. Kosinski J, Hinrichsen I, Bujnicki JM, Friedhoff P, Plotz G Hum Mutat. 2010