Publications

  • 2017
  • Budzko L, Jackowiak P, Kamel K, Sarzynska J, Bujnicki JM, Figlerowicz M. Mutations in human AID differentially affect its ability to deaminate cytidine and 5-methylcytidine in ssDNA substrates in vitro. 2017. Sci Rep, (in press) . details
  • Karlowicz A, Wegrzyn K, Gross M, Kaczynska D, Ropelewska M, Siemiątkowska M, Bujnicki JM, Konieczny I. Defining the crucial domain and amino acid residues in bacterial Lon protease for DNA binding and processing of DNA-interacting substrates. 2017. J Biol Chem, Epub ahead of print (pii: jbc.M116.766709) . details
  • Miao Z, Adamiak RW, Antczak M, Batey RT, Becka A, Biesiada M, Boniecki MJ, Bujnicki JM, Chen S, Cheng CY, Chou F, Ferré-D'Amaré AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Lach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J Jr, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B II, Xiao Y, Xu X, Zhang D, Zok T, Westhof E. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. 2017. RNA, Epub ahead of print . details
  • The RNAcentral Consortium (Petrov AI et al within Bujnicki JM) . RNAcentral: a comprehensive database of non-coding RNA sequences. 2017. Nucleic Acids Res, 45(D1):D128-D134 . details
  • 2016
  • Dawson WK, Maciejczyk M, Jankowska EJ, Bujnicki JM. Coarse-grained modeling of RNA 3D structure. 2016. Methods, 103:138-56 . details
  • Machnicka MA, Dunin-Horkawicz S, de Crécy-Lagard V, Bujnicki JM. tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs. 2016. Methods, 107:34-41 . details
  • Urulangodi M, Dhanaraju R, Gupta K, Roy RP, Bujnicki JM, Rao DN . Asymmetric DNA methylation by dimeric EcoP15I DNA methyltransferase. 2016. Biochimie, 128-129:70-82 . details
  • Pawlowski M, Kozlowski L, Kloczkowski A . MQAPsingle: A quasi single-model approach for estimation of the quality of individual protein structure models. 2016. Proteins, 84(8):1021-8 . details
  • Iskierko Z, Sharma PS, Prochowicz D, Fronc K, D'Souza F, Toczydłowska D, Stefaniak F, Noworyta K . Molecularly Imprinted Polymer (MIP) Film with Improved Surface Area Developed by Using Metal-Organic Framework (MOF) for Sensitive Lipocalin (NGAL) Determination.. 2016. ACS Appl Mater Interfaces., 8(31):19860-5 . details
  • Glow D, Kurkowska M, Czarnecka J, Szczepaniak K, Pianka D, Kappert V, Bujnicki JM, Skowronek KJ . Identification of protein structural elements responsible for the diversity of sequence preferences among Mini-III RNases.. 2016. Sci Rep., pii: gkw862 6:38612. details
  • Patel T, Chojnowski G, Astha, Koul A, McKenna S, Bujnicki JM . Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering and computational methods. 2016. Methods, in press . details
  • Van Laer B, Roovers M, Wauters L, Kasprzak JM, Dyzma M, Deyaert E, Singh R, Feller A, Bujnicki JM, Droogmans L, Versées W. Structural and functional insights into tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue. 2016. Nucleic Acids Res, 44(2):940-53 . details
  • Dawson WK, Bujnicki JM. Computational modeling of RNA 3D structures and interactions. 2016. Curr Opin Struct Biol, 37:22-28 . details
  • Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction. 2016. Nucleic Acids Res, 44(7):e63 . details
  • Ukleja M, Cuellar J, Siwaszek A, Kasprzak JM, Czarnocki-Cieciura M, Bujnicki JM, Dziembowski A, Valpuesta J. The architecture of the Schizosaccharomyces pombe CCR4-NOT complex. 2016. Nature Commun, 7:10433 . details
  • Matelska D, Kurkowska M, Purta E, Bujnicki JM, Dunin-Horkawicz S. Loss of conserved non-coding RNAs in genomes of bacterial endosymbionts. 2016. Genome Biol Evol, 8(2):426-38 . details
  • Yahara K, Furuta Y, Morimoto S, Kikutake C, Komukai S, Matelska D, Dunin-Horkawicz S, Bujnicki JM, Uchiyama I, Kobayashi I. Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori. 2016. DNA Res, 23(2):135-43 . details
  • Magnus MM, Boniecki MJ, Dawson WK, Bujnicki JM. SimRNAweb: a web server for RNA 3D structure modeling with optional restraints. 2016. Nucleic Acids Res, 44(W1):W315-9 . details
  • 2015
  • Petrov AI, Kay SJ, Gibson R, Kulesha E, Staines D, Bruford EA, Wright MW, Burge S, Finn RD, Kersey PJ, Cochrane G, Bateman A, Griffiths-Jones S, Harrow J, Chan PP, Lowe TM, Zwieb CW, Wower J, Williams KP, Hudson CM, Gutell R, Clark MB, Dinger M, Quek XC, Bujnicki JM, Chua NH, Liu J, Wang H, Skogerbø G, Zhao Y, Chen R, Zhu W, Cole JR, Chai B, Huang HD, Huang HY, Cherry J, Hatzigeorgiou A, Pruitt KD. RNAcentral: an international database of ncRNA sequences. 2015. Nucleic Acids Res, 43:D123-D129 . details
  • Zheng H, Shabalin I, Handing K, Bujnicki JM, Minor M. Magnesium binding architectures in RNA crystal structures: validation binding preferences, classification, and motif detection. 2015. Nucleic Acids Res, 43(7):3789-801 . details
  • Tuszynska I, Magnus M, Jonak K, Dawson W, Bujnicki JM. NPDock – a web server for protein-nucleic acid docking. 2015. Nucleic Acids Res, 43(W1):W425-30 . details
  • Plotka M, Kaczorowska AK, Morzywolek A, Makowska J, Kozlowski LP, Thorisdottir A, Skírnisdottir S, Hjörleifsdottir S, Fridjonsson OH, Hreggvidsson GO, Kristjansson JK, Dabrowski S, Bujnicki JM, Kaczorowski T. Biochemical Characterization and Validation of a Catalytic Site of a Highly Thermostable Ts2631 Endolysin from the Thermus scotoductus Phage vB_Tsc2631. 2015. PLoS One, 10(9):e0137374 . details
  • Philips A, Lach G, Bujnicki JM . Computational methods for prediction of RNA interactions with metal ions and small organic ligands. 2015. Methods Enzymol, 553 261-85. details
  • Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D'amaré AR, Das R, Ding F, Dokholyan NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A, Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E. RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. 2015. RNA, 21(6) 1066-84. details
  • Liu S, Mozaffari-Jovin S, Wollenhaupt J, Santos KF, Theuser M, Dunin-Horkawicz S, Fabrizio P, Bujnicki JM, Lührmann R, Wahl MC. A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing. 2015. eLife, 4:e07320 . details
  • Glow D, Pianka D, Sulej A, Kozlowski L, Czarnecka J, Chojnowski G, Skowronek KJ, Bujnicki JM. Sequence-specific cleavage of dsRNA by Mini-III RNase. 2015. Nucleic Acids Res, 43(5) 2864-73. details
  • Deo S, Patel TR, Chojnowski G, Koul A, Dzananovic E, McEleney K, Bujnicki JM, McKenna SA. Characterization of the termini of the West Nile virus genome and their interactions with the small isoform of the 2' 5'-Oligoadenylate Synthetase family. 2015. J Struct Biol, 190(2) 236-49. details
  • Czerwoniec A, Kasprzak JM, Bytner P, Dobrychlop M, Bujnicki JM. Structure and intrinsic disorder of the proteins of the Trypanosoma brucei editosome. 2015. FEBS Lett, 589(19 Pt A) 2603-10. details
  • Chojnowski G, Walen T, Piatkowski P, Potrzebowski W, Bujnicki JM. Brickworx builds recurrent RNA and DNA structural motifs into medium and low-resolution electron density maps. 2015. Acta Crystallogr D Biol Crystallogr, 71(Pt 3) 697-705. details
  • Chawla M, Oliva R, Bujnicki JM, Cavallo L. An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies. 2015. Nucleic Acids Res, 43(19) 9573. details
  • Boekema C, Owens F, Love A, Li Z, Sakkaris P, Dawson WK. A magnetic origin of cuprate superconductivity? A MaxEnt-mu SR view. 2015. Int J Mod Phys B, 29(25-26) 42026-42026. details
  • Blatter M, Dunin-Horkawicz S, Grishina I, Maris C, Thore S, Maier T, Bindereif A, Bujnicki JM, Allain FHT. The signature of the five-stranded vRRM fold defined by functional, structural and computational analysis of the hnRNP L protein. 2015. J Mol Biol, 427(19) 3001-22. details
  • Bocian-Ostrzycka KM, Łasica AM, Dunin-Horkawicz S, Grzeszczuk MJ, Drabik K, Dobosz AM, Godlewska R, Nowak E, Collet J-F, Jagusztyn-Krynicka EK. Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain. 2015. Frontiers in Microbiology, 6:1065 . details
  • Roszczenko P, Grzeszczuk M, Kobierecka P, Wywial E, Urbanowicz P, Wincek P, Nowak E, Jagusztyn-Krynicka EK . Helicobacter pylori HP0377, a member of the Dsb family, is an untypical multifunctional CcmG that cooperates with dimeric thioldisulfide oxidase HP0231. 2015. BMC Microbiol., 15 135. details
  • 2014
  • Szczepaniak K, Lach G, Bujnicki JM, Dunin-Horkawicz S. Designability landscape reveals sequence features that define axial helix rotation in four-helical homo-oligomeric antiparallel coiled-coil structures. 2014. J Struct Biol., 188(2) 123-33. details
  • Grabowska AD, Wywiał E, Dunin-Horkawicz S , Lasica AM, Wösten MM, Nagy-Staroń A, Godlewska R, Bocian-Ostrzycka K, Pieńkowska K, Laniewski P, Bujnicki JM, van Putten JP, Jagusztyn-Krynicka EK . Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. 2014. PLoS One., 9(9) e106247. details
  • Walen T, Chojnowski G, Gierski P,Bujnicki JM, . ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes. 2014. Nucleic Acids Res., 42(19) e151. details
  • Ramos-Molina B, Lambertos A, Lopez-Contreras AJ, Kasprzak JM, Czerwoniec A, Bujnicki JM, Cremades A, Penafiel R. Structural and degradative aspects of ornithine decarboxylase antizyme inhibitor 2. 2014. FEBS Open Bio., 4 510-21. details
  • Sierocka I, Kozlowski LP, Bujnicki JM, Jarmolowski A, Szweykowska-Kulinska Z . Female-specific gene expression in dioecious liverwort Pellia endiviifolia is developmentally regulated and connected to archegonia production. 2014. BMC Plant Biol., 14(1) 168. details
  • Magnus M, Matelska D, Lach G, Chojnowski G, Boniecki MJ, Purta E, Dawson W, Dunin-Horkawicz S, Bujnicki JM . Computational modeling of RNA 3D structures, with the aid of experimental restraints. 2014. RNA Biol., 11(5) 522-36. details
  • Rother K, Rother M, Skiba P, Bujnicki JM. Automated modeling of RNA 3D structure. 2014. Methods Mol Biol, 1097 395-415. details
  • Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler M. Structural basis of the methylation specificity of R.DpnI. 2014. Nucleic Acids Res., 42(13) 8745-54. details
  • Majorek KA, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A, Nowotny M, Ginalski K, Bujnicki JM. The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification. 2014. Nucleic Acids Res., 42(7) 4160-79. details
  • Toczyłowska-Mamińska R, Olszewska A, Laskowski M, Bednarczyk P, Skowronek K, Szewczyk A. Potassium channel in the mitochondria of human keratinocytes. 2014. J Invest Dermatol, 134(3) 764-72. details
  • Sadowski Ł, Jastrzębski K, Purta E, Hellberg C, Miaczynska M. Labeling of platelet-derived growth factor by reversible biotinylation to visualize its endocytosis by microscopy. 2014. Methods Enzymol., 535 167-77. details
  • Crochemore M, Iliopoulos CS, Kubica M, Radoszewski J, Rytter W, Stencel K, Walen T. New simple efficient algorithms computing powers and runs in strings. 2014. Discrete Applied Mathematics, 163(3) 258–267. details
  • Smietanski M, Werner M, Purta E, Kaminska KH, Stepinski J, Darzynkiewicz E, Nowotny M, Bujnicki JM. Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation. 2014. Nat Commun, 5 3004. details
  • Chojnowski G, Walen T, Bujnicki JM. RNA Bricks - a database of RNA 3D motifs and their interactions. 2014. Nucleic Acids Res., 42(1) D123-31. details
  • Dzananovic E, Patel TR, Chojnowski G, Boniecki MJ, Deo S, McEleney K, Harding SE, Bujnicki JM, McKenna SA. Solution conformation of Adenovirus Virus Associated RNA-I and its interaction with PKR. 2014. J Struct Biol, 185(1) 48-57. details
  • Plotka M, Kaczorowska AK, Stefanska A, Morzywolek A, Fridjonsson OH, Dunin-Horkawicz S, Kozlowski L, Hreggvidsson GO, Kristjansson JK, Dabrowski S, Bujnicki JM, Kaczorowski T. Novel Highly Thermostable Endolysin from Thermus scotoductus MAT2119 Bacteriophage Ph2119 with Amino Acid Sequence Similarity to Eukaryotic Peptidoglycan Recognition Proteins. 2014. Appl Environ Microbiol, 80(3) 886-95. details
  • Tuszynska I, Matelska D, Magnus M, Chojnowski G, Kasprzak JM, Kozlowski LP, Dunin-Horkawicz S, Bujnicki JM. Computational modeling of protein-RNA complex structures. 2014. Methods, 65(3) 310-9. details
  • 2013
  • Xu C, Liu R, Mehta AK, Guerrero-Ferreira RC, Wright ER, Dunin-Horkawicz S, Morris K, Serpell LC, Zuo X, Wall JS, Conticello VP. Rational design of helical nanotubes from self-assembly of coiled-coil lock washers. 2013. J Am Chem Soc., 135(41) 15565-78. details
  • Philips A, Milanowska K, Lach G, Bujnicki JM. LigandRNA: computational predictor of RNA-ligand interactions. 2013. RNA, 19(12) 1605-16. details
  • Czeredys M, Samluk L, Michalec K, Tułodziecka K, Skowronek K, Nałęcz KA. Caveolin-1 - a novel interacting partner of organic cation/carnitine transporter (octn2): effect of protein kinase C on this interaction in rat astrocytes.. 2013. PLoS One, 8(12) e82105. details
  • Matelska D, Purta E, Panek S, Boniecki MJ, Bujnicki JM, Dunin-Horkawicz S. S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA. 2013. RNA, 19(10) 1341-8. details
  • Kubica M, Kulczyńskia T, Radoszewskia J, Rytter W,Walen T. A linear time algorithm for consecutive permutation pattern matching. 2013. Information Processing Letters, 113(12) 430-433. details
  • Bednarczyk P, Wieckowski MR, Broszkiewicz M, Skowronek K, Siemen D, Szewczyk A. Putative Structural and Functional Coupling of the Mitochondrial BKCa Channel to the Respiratory Chain. 2013. PLoS One, 8(6) e68125. details
  • Crochemore M, Iliopoulos C.S, Kociumaka T, Kubica M, Pachocki J, Radoszewski J, Rytter W,Tyczyński W, Waleń T. A note on efficient computation of all Abelian periods in a string. 2013. Information Processing Letters, 113(3) 74-77. details
  • Pawlowski M, Bogdanowicz A, Bujnicki JM. QA-RecombineIt: a server for quality assessment and recombination of protein models. 2013. Nucleic Acids Res, 41(Web Server issue) W389-97. details
  • Lukasiak P, Antczak M, Ratajczak T, Bujnicki JM, Szachniuk M, Adamiak RW, Popenda M, Blazewicz J. RNAlyzer--novel approach for quality analysis of RNA structural models. 2013. Nucleic Acids Res, 41(12) 5978-90. details
  • Bujnicki JM, Tiuryn J. Bioinformatics and computational biology in Poland. 2013. PLoS Comput Biol, 9(5) e1003048. details
  • Puton T, Kozlowski LP, Rother KM, Bujnicki JM. CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction. 2013. Nucleic Acids Res., 41(7) 4307-23. details
  • Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M. Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. 2013. Nucleic Acids Res, 41(6) 3874-87. details
  • Milanowska K, Mikolajczak K, Lukasik A, Skorupski M, Balcer Z, Machnicka MA, Nowacka M, Rother KM, Bujnicki JM. RNApathwaysDB – a database of RNA maturation and decay pathways. 2013. Nucleic Acids Res, 41(D1) D268-72. details
  • Machnicka MA, Milanowska K, Osman Oglou O, Purta E, Kurkowska M, Olchowik A, Januszewski W, Kalinowski S, Dunin-Horkawicz S, Rother KM, Helm M, Bujnicki JM, Grosjean H. MODOMICS: a database of RNA modification pathways: 2013 update. 2013. Nucleic Acids Res, 41(D1) D262-7. details
  • 2012
  • Kozlowski L, Orlowski J, Bujnicki JM. Structure prediction of alternatively spliced proteins In „Alternative pre-mRNA Splicing: Theory and Protocols: The Complete Guide for Biomedical Scientists”. 2012. , . details
  • Rother K, Rother M, Boniecki M, Puton T, Tomala K, Lukasz P, Bujnicki JM. Template-based and template-free modeling of RNA 3D structure: inspirations from protein structure modeling In "RNA Structure Prediction and Modelling". 2012. , . details
  • Kozlowski LP, Bujnicki JM. MetaDisorder: A meta-server for the prediction of intrinsic disorder in proteins. 2012. BMC Bioinformatics, 13 111. details
  • Kasprzak JM, Czerwoniec A, Bujnicki JM. Molecular evolution of dihydrouridine synthases. 2012. BMC Bioinformatics, 13 153. details
  • Korneta I, Bujnicki JM. Intrinsic disorder in the human spliceosomal proteome. 2012. PLoS Comput Biol, 8(8) e1002641. details
  • Kusio-Kobialka M, Wolanin K, Podszywalow-Bartnicka P, Sikora E, Skowronek K, McKenna SL, Ghizzoni M, Dekker FJ, Piwocka K. Increased acetylation of lysine 317/320 of p53 caused by BCR-ABL protects from cytoplasmic translocation of p53 and mitochondria-dependent apoptosis in response to DNA damage. 2012. Apoptosis, 17(9) 950-63. details
  • Roszczenko P, Radomska KA, Wywial E, Collet JF, Jagusztyn-Krynicka EK. A novel insight into the oxidoreductase activity of Helicobacter pylori HP0231 protein. 2012. PLoS One, 7(10) e46563. details
  • Al-Haggar M, Madej-Pilarczyk A, Kozlowski L, Bujnicki JM, Yahia S, Abdel-Hadi D, Shams A, Ahmad N, Hamed S, Puzianowska-Kuznicka M. A novel homozygous p.Arg527Leu LMNA mutation in two unrelated egyptian families causes overlapping mandibuloacral dysplasia and progeria syndrome. 2012. Eur J Hum Genet, 20(11) 1134-40. details
  • Magnus M, Pawlowski M, Bujnicki JM. MetaLocGramN: A meta-predictor of protein subcellular localization for Gram-negative bacteria. 2012. Biochim Biophys Acta, 1824(12) 1425-33. details
  • Skowronek K, Boniecki MJ, Kluge B, Bujnicki JM. Rational engineering of sequence specificity in R.MwoI restriction endonuclease. 2012. Nucleic Acids Res, 40(17) 8579-92. details
  • Poleszak K, Kaminska KH, Dunin-Horkawicz S, Lupas A, Skowronek KJ, Bujnicki JM. Delineation of structural domains and identification of functionally important residues in DNA repair enzyme Exonuclease VII. 2012. Nucleic Acids Res, 40(16) 8163-74. details
  • Korneta I, Magnus M, Bujnicki JM. Structural bioinformatics of the human spliceosomal proteome. 2012. Nucleic Acids Res, 40(15) 7046-65. details
  • Drozdz M, Piekarowicz A, Bujnicki JM, Radlinska M. Novel non-specific DNA adenine methyltransferases. 2012. Nucleic Acids Res, 40(5) 2119-30. details
  • Sulej AA, Tuszynska I, Skowronek KJ, Nowotny M, Bujnicki JM. Sequence-specific cleavage of the RNA strand in DNA-RNA hybrids by the fusion of ribonuclease H with a zinc finger. 2012. Nucleic Acids Res, 40(22) 11563-70. details
  • Pawlowski M, Bujnicki JM. The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement. 2012. BMC Bioinformatics, 13(1) 289. details
  • Pietal MJ, Szostak N, Rother KM, Bujnicki JM. RNAmap2D -- calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures. 2012. BMC Bioinformatics, 13(1) 333. details
  • Siwek W, Czapinska H, Bochtler M, Bujnicki JM, Skowronek K. Crystal structure and mechanism of action of the N6-methyladenine dependent type IIM restriction endonuclease. 2012. Nucleic Acids Res, 40(15) 7563-72. details
  • Samluk L, Czeredys M, Skowronek K, Nałęcz KA. Protein kinase C regulates amino acid transporter ATB. 2012. Biochem Biophys Res Commun., 422(1) 64-9. details
  • Malenda A, Skrobanska A, Issat T, Winiarska M, Bil J, Oleszczak B, Sinski M, Firczuk M, Bujnicki JM, Chlebowska J, Staruch AD, Glodkowska-Mrowka E, Kunikowska J, Krolicki L, Szablewski L, Gaciong Z, Koziak K, Jakobisiak M, Golab J, Nowis DA. Statins Impair Glucose Uptake in Tumor Cells. 2012. Neoplasia, 14 311-23. details
  • Lach G, DeKievet M, Jentschura UD. Einstein–Hopf drag, Doppler shift of thermal radiation and blackbody drag: Three perspectives on quantum friction. 2012. Cent. Eur. J. Phys., 10(4) 763-767. details
  • Fislage M, Roovers M, Tuszynska I, Bujnicki JM, Droogmans L, Versées W. Crystal structures of the tRNA:m(2)G6 methyltransferase Trm14/TrmN from two domains of life. 2012. Nucleic Acids Res, 40(11) 5149-61. details
  • Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, Patel DJ, Philips A, Puton T, Santalucia J, Sijenyi F, Hermann T, Rother K, Rother M, Serganov A, Skorupski M, Soltysinski T, Sripakdeevong P, Tuszynska I, Weeks KM, Waldsich C, Wildauer M, Leontis NB, Westhof E. RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction. 2012. RNA, 18 610-25. details
  • Chojnowski G, Bujnicki JM, Bochtler M. RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes. 2012. Bioinformatics, 28(6) 880-1. details
  • Zylicz-Stachula A, Zolnierkiewicz O, Lubys A, Ramanauskaite D, Mitkaite G, Bujnicki JM, Skowron P. Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities. 2012. BMC Mol Biol, 13(1) 13. details
  • Roovers M, Oudjama Y, Fislage M, Bujnicki JM, Versées W, Droogmans L. The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N2-methylguanosine at position 6 in tRNA. 2012. RNA, 18(4) 815-24. details
  • Nakagome S, Mano S, Kozlowski L, Bujnicki JM, Shibata H, Fukumaki Y, Kidd JR, Kidd KK, Kawamura S, Oota H. Crohn's Disease Risk Alleles on the NOD2 Locus Have Been Maintained by Natural Selection on Standing Variation. 2012. Mol Biol Evol, 29(6) 1569-85. details
  • Puton T, Kozlowski L, Tuszynska I, Rother K, Bujnicki JM. Computational methods for prediction of protein-RNA interactions. 2012. J Struct Biol, 179(3) 261-8. details
  • Rother K, Potrzebowski W, Puton T, Rother M, Wywial E, Bujnicki JM . A toolbox for developing bioinformatics software. 2012. Brief Bioinform, 13(2) 244-57. details
  • Kennaway CK, Taylor JE, Song CF, Potrzebowski W, Nicholson W, White JH, Swiderska A,Obarska-Kosinska A, Callow P, Cooper LP, Roberts GA, Artero JB,Bujnicki JM, Trinick J, Kneale GG, Dryden DT. Structure and operation of the DNA-translocating type I DNA restriction enzymes. 2012. Genes Dev, 26(1) 92-104. details
  • Philips A, Milanowska K, Lach G, Boniecki M, Rother K, Bujnicki JM. MetalionRNA: computational predictor of metal-binding sites in RNA structures. 2012. Bioinformatics, 28(2) 198-205. details
  • 2011
  • Bielska E, Lucas X, Czerwoniec A, Kasprzak JM, Kaminska KH, Bujnicki JM. Virtual screening strategies in drug design - methods and applications. 2011. BioTechnologia, 92(3) 249-264. details
  • Sikorski K, Czerwoniec A, Bujnicki JM, Wesoly J, Bluyssen HAR. STAT1 as a novel therapeutical target in pro-atherogenic signal integration of IFNg, TLR4 and IL-6 in vascular disease. 2011. Cytokine Growth Factor Rev., 22(4) 211-9. details
  • Rother M, Rother K, Puton T, Bujnicki JM. RNA tertiary structure prediction with ModeRNA. 2011. Brief Bioinform, 12(6) 601-13. details
  • Milanowska K, Rother K, Bujnicki JM. Databases and bioinformatics tools for the study of DNA repair. 2011. Mol Biol Int, 475718 . details
  • Liu J, Ganapathy K, Wywial E, Bujnicki JM, Nwogwugwu CA, Nes WD. Effect of substrate features and mutagenesis of active site tyrosine residues on the reaction course catalysed by Trypanosoma brucei sterol C-24-methyltransferase. 2011. Biochem J, 439(3) 413-22. details
  • Czerwoniec A, Bujnicki JM. Identification and modeling of a phosphatase-like domain in a tRNA 2'-O-ribosyl phosphate transferase Rit1p. 2011. Cell Cycle, 10(20) 3566-70. details
  • 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. RNAcentral: A vision for an international database of RNA sequences. 2011. RNA, 17(11) 1941-6. details
  • Rother M, Rother K, Puton T, Bujnicki JM. ModeRNA: a tool for comparative modeling of RNA 3D structure. 2011. Nucleic Acids Res, 39(10) 4007-4022. details
  • Werner M, Purta E, Kaminska KH, Cymerman IA, Campbell DA, Mittra B, Zamudio JR, Sturm NR, Jaworski J, Bujnicki JM. 2'-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family. 2011. Nucleic Acids Res, 39(11) 4756-4768. details
  • Tuszynska I, Bujnicki JM. DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking. 2011. BMC Bioinformatics, 12 348. details
  • Rother M, Milanowska K, Puton T, Jeleniewicz J, Rother K, Bujnicki JM. ModeRNA server: an online tool for modeling RNA 3D structures. 2011. Bioinformatics, 27(17) 2441-2442. details
  • Rother K, Rother M, Boniecki M, Puton T, Bujnicki JM. RNA and protein 3D structure modeling: similarities and differences. 2011. J Mol Model., 17(9) 2325-2336. details
  • Spears JL, Rubio MA, Gaston KW, Wywial E, Strikoudis A, Bujnicki JM, Papavasiliou FN, Alfonzo JD. A single zinc ion is sufficient for an active Trypanosoma brucei tRNA editing deaminase. 2011. J Biol Chem, 286(23) 20366-74. details
  • Tesfazgi Mebrhatu M, Wywial E, Ghosh A, Michiels CW, Lindner AB, Taddei F, Bujnicki JM, Van Melderen L, Aertsen A. Evidence for an evolutionary antagonism between Mrr and Type III modification systems.. 2011. Nucleic Acids Res, 39(14) 5991-6001. details
  • Rother K, Rother M, Boniecki M, Puton T, Tomala K, Lukasz P, Bujnicki JM. Template-based and template-free modeling of RNA 3D structure: inspirations from protein structure modeling. 2011. RNA Structure Prediction and Modelling, 27 67-90. details
  • Kozlowski L, Orlowski J, Bujnicki JM. Structure prediction of alternatively spliced proteins. 2011. RNA splicing: The complete guide, 582-591. details
  • Husain N, Obranic S, Koscinski L, Seetharaman J, Babic F, Bujnicki JM, Maravic-Vlahovicek G, Sivaraman J. 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. 2011. Nucleic Acids Res, 39(5) 1903-18. details
  • 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. "4D Biology for health and disease" workshop report. 2011. N Biotechnol, 28(4) 291-3. details
  • Milanowska K, Krwawicz J, Papaj G, Kosinski J, Poleszak K, Lesiak J, Osinska E, Rother K, Bujnicki JM. REPAIRtoire-a database of DNA repair pathways. 2011. Nucleic Acids Res, 39 D788-D792. details
  • 2010
  • Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA. BioCatalogue: a universal catalogue of web services for the life sciences. 2010. Nucleic Acids Res, 38(Web Server issue) W689-94. details
  • Tkaczuk KL. Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site. 2010. J Mol Model., 16(3) 599-606. details
  • Rother K, Hoffmann S, Bulik S, Hoppe A, Gasteiger J, Holzhütter HG. IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities. 2010. Biophys J., 98(11) 2478-86. details
  • Khan F, Furuta Y, Kawai M, Kaminska KH, Ishikawa K, Bujnicki JM, Kobayashi I. A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI).. 2010. Nucleic Acids Res, 38 3019-30. details
  • Tuszynska I, Bujnicki JM. Predicting atomic details of the unfolding pathway for YibK, a knotted protein from the SPOUT superfamily. 2010. J Biomol Struct Dyn, 27 511-20. details
  • Kaminska KH, Purta E, Hansen LH, Bujnicki JM, Vester B, Long KS. Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria.. 2010. Nucleic Acids Res, 38 1652-63. details
  • Zhou X, Chua TK, Tkaczuk KL, Bujnicki JM, Sivaraman J. The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket.. 2010. J Struct Biol, 169 277-85. details
  • Pukáncsik M, Békési A, Klement E, Hunyadi-Gulyás E, Medzihradszky KF, Kosinski J, Bujnicki JM, Alfonso C, Rivas G, Vértessy BG. Physiological truncation and domain organization of a novel uracil-DNA-degrading factor.. 2010. FEBS J, 277 1245-59. details
  • Zhang Z, Theler D, Kaminska KH, Hiller M, de la Grange P, Pudimat R, Rafalska I, Heinrich B, Bujnicki JM, Allain FH, Stamm S. The YTH domain is a novel RNA binding domain.. 2010. J Biol Chem, 285 14701-10. details
  • Pukszta S, Schilke B, Dutkiewicz R, Kominek J, Moczulska K, Stepien B, Reitenga KG, Bujnicki JM, Williams B, Craig EA, Marszalek J. Co-evolution-driven switch of J-protein specificity towards an Hsp70 partner.. 2010. EMBO Rep, 11 360-5. details
  • Kempenaers M, Roovers M, Oudjama Y, Tkaczuk KL, Bujnicki JM, Droogmans L. New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA.. 2010. Nucleic Acids Res, 38 6533-43. details
  • Husain N, Tkaczuk KL, Tulsidas SR, Kaminska KH, Cubrilo S, Maravić-Vlahovicek G, Bujnicki JM, Sivaraman J. 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.. 2010. Nucleic Acids Res, 38 4120-32. details
  • Kosinski J, Hinrichsen I, Bujnicki JM, Friedhoff P, Plotz G. Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair.. 2010. Hum Mutat, 31 975-82. details
  • Chua TK, Seetharaman J, Kasprzak JM, Ng C, Patel BK, Love C, Bujnicki JM, Sivaraman J. Crystal structure of a fructokinase homolog from Halothermothrix orenii. 2010. J Struct Biol, 171 397-401. details
  • Gajda MJ, Tuszynska I, Kaczor M, Bakulina AY, Bujnicki JM. FILTREST3D: discrimination of structural models using restraints from experimental data.. 2010. Bioinformatics, 26 2986-7. details
  • 2009
  • Majorek KA, Bujnicki JM. Modeling of Escherichia coli Endonuclease V structure in complex with DNA.. 2009. J Mol Model, 15 173-82. details
  • Fink G, Hajdo L, Skowronek KJ, Reuther C, Kasprzak AA, Diez S. The mitotic kinesin-14 Ncd drives directional microtubule-microtubule sliding.. 2009. Nat Cell Biol, 11 717-23. details
  • Czerwoniec A, Dunin-Horkawicz S, Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Grosjean H, Rother K. MODOMICS: a database of RNA modification pathways. 2008 update. 2009. Nucleic Acids Res, 37 D118-21. details
  • Nakonieczna J, Kaczorowski T, Obarska-Kosinska A, Bujnicki JM. Functional analysis of MmeI from methanol utilizer Methylophilus methylotrophus, a subtype IIC restriction-modification enzyme related to type I enzymes.. 2009. Appl Environ Microbiol, 75 212-23. details
  • Kennaway CK, Obarska-Kosinska A, White JH, Tuszynska I, Cooper LP, Bujnicki JM, Trinick J, Dryden DT. The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein. 2009. Nucleic Acids Res, 37 762-70. details
  • Pierechod M, Nowak A, Saari A, Purta E, Bujnicki JM, Konieczny I. Conformation of a plasmid replication initiator protein affects its proteolysis by ClpXP system. 2009. Protein Sci, 18 637-49. details
  • Matsumoto Y, Oota H, Asaoka Y, Nishina H, Watanabe K, Bujnicki JM, Oda S, Kawamura S, Mitani H. Medaka: a promising model animal for comparative population genomics.. 2009. BMC Res Notes, 2 88. details
  • Bauer RA, Rother K, Moor P, Reinert K, Steinke T, Bujnicki JM. Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors. 2009. Algorithms, 2(2) 692-709. details
  • Purta E, O'Connor M, Bujnicki JM, Douthwaite S. YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA.. 2009. Mol Microbiol, 72 1147-58. details
  • Pawłowski M, Lasica AM, Jagusztyn-Krynicka EK, Bujnicki JM. AAN82231 protein from uropathogenic E. coli CFT073 is a close paralog of DsbB enzymes and does not belong to the DsbI family. 2009. Pol J Microbiol, 58 181-4. details
  • Zylicz-Stachula A, Bujnicki JM, Skowron PM. Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family.. 2009. BMC Mol Biol, 10 52. details
  • Palfi Z, Jaé N, Preusser C, Kaminska KH, Bujnicki JM, Lee JH, Günzl A, Kambach C, Urlaub H, Bindereif A. SMN-assisted assembly of snRNP-specific Sm cores in trypanosomes.. 2009. Genes Dev, 23 1650-64. details
  • Pena V, Jovin SM, Fabrizio P, Orlowski J, Bujnicki JM, Lührmann R, Wahl MC. Common design principles in the spliceosomal RNA helicase Brr2 and in the Hel308 DNA helicase.. 2009. Mol Cell, 35 454-66. details
  • Kolmos E, Nowak M, Werner M, Fischer K, Schwarz G, Mathews S, Schoof H, Nagy F, Bujnicki JM, Davis SJ. Integrating ELF4 into the circadian system through combined structural and functional studies.. 2009. HFSP J, 3 350-66. details
  • Leski TA, Caswell CC, Pawlowski M, Klinke DJ, Bujnicki JM, Hart SJ, Lukomski S. Identification and classification of bcl genes and proteins of Bacillus cereus group organisms and their application in Bacillus anthracis detection and fingerprinting.. 2009. Appl Environ Microbiol, 75 7163-72. details
  • 2008
  • Maravić Vlahovicek G, Cubrilo S, Tkaczuk KL, Bujnicki JM. Modeling and experimental analyses reveal a two-domain structure and amino acids important for the activity of aminoglycoside resistance methyltransferase Sgm.. 2008. Biochim Biophys Acta, 1784 582-90. details
  • Vasu K, Saravanan M, Bujnicki JM, Nagaraja V. Structural integrity of the beta beta alpha-Metal finger motif is required for DNA binding and stable protein-DNA complex formation in R.KpnI.. 2008. Biochim Biophys Acta, 1784 269-75. details
  • Kaminska KH, Baraniak U, Boniecki M, Nowaczyk K, Czerwoniec A, Bujnicki JM. Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms(2)io(6)A37 in tRNA.. 2008. Proteins, 70 1-18. details
  • Roovers M, Oudjama Y, Kaminska KH, Purta E, Caillet J, Droogmans L, Bujnicki JM. Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA.. 2008. Proteins, 71 2076-85. details
  • Kaminska KH, Bujnicki JM. Bacteriophage Mu Mom protein responsible for DNA modification is a new member of the acyltransferase superfamily.. 2008. Cell Cycle, 7 120-1. details
  • Mittra B, Zamudio JR, Bujnicki JM, Stepinski J, Darzynkiewicz E, Campbell DA, Sturm NR. The TbMTr1 spliced leader RNA cap 1 2'-O-ribose methyltransferase from Trypanosoma brucei acts with substrate specificity. 2008. J Biol Chem, 283 3161-72. details
  • Feder M, Purta E, Koscinski L, Cubrilo S, Maravic Vlahovicek G, Bujnicki JM. Virtual screening and experimental verification to identify potential inhibitors of the ErmC methyltransferase responsible for bacterial resistance against macrolide antibiotics.. 2008. ChemMedChem, 3 316-22. details
  • Bhagwat AS, Carpenter MA, Bujnicki JM. Is AID a monomer in solution?. 2008. DNA Repair (Amst), 7 349-50; author reply 351-2. details
  • Cymerman IA, Chung I, Beckmann BM, Bujnicki JM, Meiss G. EXOG, a novel paralog of Endonuclease G in higher eukaryotes.. 2008. Nucleic Acids Res, 36 1369-79. details
  • Sen TZ, Kloster M, Jernigan RL, Kolinski A, Bujnicki JM, Kloczkowski A. Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA.. 2008. Biophys J, 94 2482-91. details
  • Chua TK, Bujnicki JM, Tan TC, Huynh F, Patel BK, Sivaraman J. The structure of sucrose phosphate synthase from Halothermothrix orenii reveals its mechanism of action and binding mode.. 2008. Plant Cell, 20 1059-72. details
  • Roovers M, Kaminska KH, Tkaczuk KL, Gigot D, Droogmans L, Bujnicki JM. The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK).. 2008. Nucleic Acids Res, 36 3252-62. details
  • Orlowski J, Bujnicki JM. Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.. 2008. Nucleic Acids Res, 36 3552-69. details
  • White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM, Johnson AW. Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits.. 2008. Mol Cell Biol, 28 3151-61. details
  • Kosinski J, Plotz G, Guarné A, Bujnicki JM, Friedhoff P. The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family.. 2008. J Mol Biol, 382 610-27. details
  • Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Douthwaite S. YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA.. 2008. RNA, 14 2234-44. details
  • Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM. MetaMQAP: a meta-server for the quality assessment of protein models.. 2008. BMC Bioinformatics, 9 403. details
  • Sunita S, Tkaczuk KL, Purta E, Kasprzak JM, Douthwaite S, Bujnicki JM, Sivaraman J. Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes.. 2008. J Mol Biol, 383 652-66. details
  • Obarska-Kosinska A, Taylor JE, Callow P, Orlowski J, Bujnicki JM, Kneale GG. HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling.. 2008. J Mol Biol, 376 438-52. details
  • Purta E, O\'Connor M, Bujnicki JM, Douthwaite S. YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962. 2008. J Mol Biol, 383 641-51. details
  • Gyrd-Hansen M, Darding M, Miasari M, Santoro MM, Zender L, Xue W, Tenev T, da Fonseca PC, Zvelebil M, Bujnicki JM, Lowe S, Silke J, Meier P. IAPs contain an evolutionarily conserved ubiquitin-binding domain that regulates NF-kappaB as well as cell survival and oncogenesis.. 2008. Nat Cell Biol, 10 1309-17. details
  • Orlowski J, Mebrhatu MT, Michiels CW, Bujnicki JM, Aertsen A. Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr.. 2008. Biochem Biophys Res Commun, 377 862-6. details
  • 2007
  • Zamudio JR, Mittra B, Foldynová-Trantírková S, Zeiner GM, Lukes J, Bujnicki JM, Sturm NR, Campbell DA. The 2'-O-ribose methyltransferase for cap 1 of spliced leader RNA and U1 small nuclear RNA in Trypanosoma brucei. 2007. Mol Cell Biol, 27 6084-92. details
  • Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM. Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.. 2007. BMC Bioinformatics, 8 73. details
  • Sunita S, Purta E, Durawa M, Tkaczuk KL, Swaathi J, Bujnicki JM, Sivaraman J. Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC.. 2007. Nucleic Acids Res, 35 4264-74. details
  • Schäfer P, Cymerman IA, Bujnicki JM, Meiss G. Human lysosomal DNase IIalpha contains two requisite PLD-signature (HxK) motifs: evidence for a pseudodimeric structure of the active enzyme species.. 2007. Protein Sci, 16 82-91. details
  • Sasin JM, Godzik A, Bujnicki JM. SURF'S UP! - protein classification by surface comparisons. 2007. J Biosci, 32 97-100. details
  • Sabates-Bellver J, Van der Flier LG, de Palo M, Cattaneo E, Maake C, Rehrauer H, Laczko E, Kurowski MA, Bujnicki JM, Menigatti M, Luz J, Ranalli TV, Gomes V, Pastorelli A, Faggiani R, Anti M, Jiricny J, Clevers H, Marra G. Transcriptome profile of human colorectal adenomas.. 2007. Mol Cancer Res, 5 1263-75. details
  • Pietal MJ, Tuszynska I, Bujnicki JM. PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure.. 2007. Bioinformatics, 23 1429-30. details
  • Pena V, Liu S, Bujnicki JM, Lührmann R, Wahl MC. Structure of a multipartite protein-protein interaction domain in splicing factor prp8 and its link to retinitis pigmentosa.. 2007. Mol Cell, 25 615-24. details
  • Ozanick SG, Bujnicki JM, Sem DS, Anderson JT. Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding.. 2007. Nucleic Acids Res, 35 6808-19. details
  • Orlowski J, Boniecki M, Bujnicki JM. I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition. 2007. Bioinformatics, 23 527-30. details
  • Miyazono K, Watanabe M, Kosinski J, Ishikawa K, Kamo M, Sawasaki T, Nagata K, Bujnicki JM, Endo Y, Tanokura M, Kobayashi I. Novel protein fold discovered in the PabI family of restriction enzymes.. 2007. Nucleic Acids Res, 35 1908-18. details
  • Liu Y, Li Z, Lin Q, Kosinski J, Seetharaman J, Bujnicki JM, Sivaraman J, Hew CL. Structure and evolutionary origin of Ca(2+)-dependent herring type II antifreeze protein.. 2007. PLoS One, 2 e548. details
  • Kudan EV, Brevnov MG, Subach OM, Rechkoblit OA, Buĭnitskiĭ IaM, Gromova ES. [Probing of contacts between EcoRII DNA methyltransferase and DNA using substrate analogs and molecular modeling].. 2007. Mol Biol (Mosk), 41 885-99. details
  • Kosinski J, Kubareva E, Bujnicki JM. A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering.. 2007. Proteins, 68 324-36. details
  • Koscinski L, Feder M, Bujnicki JM. Identification of a missing sequence and functionally important residues of 16S rRNA:m(1)A1408 methyltransferase KamB that causes bacterial resistance to aminoglycoside antibiotics.. 2007. Cell Cycle, 6 1268-71. details
  • Jakubauskas A, Giedriene J, Bujnicki JM, Janulaitis A. Identification of a single HNH active site in type IIS restriction endonuclease Eco31I. 2007. J Mol Biol, 370 157-69. details
  • Ibryashkina EM, Zakharova MV, Baskunov VB, Bogdanova ES, Nagornykh MO, Den\'mukhamedov MM, Melnik BS, Kolinski A, Gront D, Feder M, Solonin AS, Bujnicki JM. Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily.. 2007. BMC Struct Biol, 7 48. details
  • Chovancová E, Kosinski J, Bujnicki JM, Damborský J. Phylogenetic analysis of haloalkane dehalogenases.. 2007. Proteins, 67 305-16. details
  • 2006
  • Zegers I, Gigot D, van Vliet F, Tricot C, Aymerich S, Bujnicki JM, Kosinski J, Droogmans L. Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase.. 2006. Nucleic Acids Res, 34 1925-34. details
  • Zamudio JR, Mittra B, Zeiner GM, Feder M, Bujnicki JM, Sturm NR, Campbell DA. Complete cap 4 formation is not required for viability in Trypanosoma brucei.. 2006. Eukaryot Cell, 5 905-15. details
  • Tkaczuk KL, Obarska A, Bujnicki JM. Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis.. 2006. BMC Evol Biol, 6 6. details
  • Skowronek KJ, Kosinski J, Bujnicki JM. Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis.. 2006. Proteins, 63 1059-68. details
  • Sikora E, Bielak-Zmijewska A, Magalska A, Piwocka K, Mosieniak G, Kalinowska M, Widlak P, Cymerman IA, Bujnicki JM. Curcumin induces caspase-3-dependent apoptotic pathway but inhibits DNA fragmentation factor 40/caspase-activated DNase endonuclease in human Jurkat cells.. 2006. Mol Cancer Ther, 5 927-34. details
  • Samaranayake M, Bujnicki JM, Carpenter M, Bhagwat AS. Evaluation of molecular models for the affinity maturation of antibodies: roles of cytosine deamination by AID and DNA repair.. 2006. Chem Rev, 106 700-19. details
  • Purta E, van Vliet F, Tkaczuk KL, Dunin-Horkawicz S, Mori H, Droogmans L, Bujnicki JM. The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase.. 2006. BMC Mol Biol, 7 23. details
  • Obarska A, Blundell A, Feder M, Vejsadová S, Sisáková E, Weiserová M, Bujnicki JM, Firman K. Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA.. 2006. Nucleic Acids Res, 34 1992-2005. details
  • Mikula M, Karczmarski J, Dzwonek A, Rubel T, Hennig E, Dadlez M, Bujnicki JM, Bomsztyk K, Ostrowski J. Casein kinases phosphorylate multiple residues spanning the entire hnRNP K length.. 2006. Biochim Biophys Acta, 1764 299-306. details
  • Metz J, Wächter A, Schmidt B, Bujnicki JM, Schwappach B. The yeast Arr4p ATPase binds the chloride transporter Gef1p when copper is available in the cytosol.. 2006. J Biol Chem, 281 410-7. details
  • Klimek-Tomczak K, Mikula M, Dzwonek A, Paziewska A, Karczmarski J, Hennig E, Bujnicki JM, Bragoszewski P, Denisenko O, Bomsztyk K, Ostrowski J. Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.. 2006. Br J Cancer, 94 586-92. details
  • Han R, Caswell CC, Lukomska E, Keene DR, Pawlowski M, Bujnicki JM, Kim JK, Lukomski S. Binding of the low-density lipoprotein by streptococcal collagen-like protein Scl1 of Streptococcus pyogenes.. 2006. Mol Microbiol, 61 351-67. details
  • Gros L, Renodon-Cornière A, de Saint Vincent BR, Feder M, Bujnicki JM, Jacquemin-Sablon A. Characterization of prmt7alpha and beta isozymes from Chinese hamster cells sensitive and resistant to topoisomerase II inhibitors.. 2006. Biochim Biophys Acta, 1760 1646-56. details
  • Godlewska R, Dzwonek A, Mikuła M, Ostrowski J, Pawłowski M, Bujnicki JM, Jagusztyn-Krynicka EK. Helicobacter pylori protein oxidation influences the colonization process.. 2006. Int J Med Microbiol, 296 321-4. details
  • Gabant G, Auxilien S, Tuszynska I, Locard M, Gajda MJ, Chaussinand G, Fernandez B, Dedieu A, Grosjean H, Golinelli-Pimpaneau B, Bujnicki JM, Armengaud J. THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain.. 2006. Nucleic Acids Res, 34 2483-94. details
  • Dunin-Horkawicz S, Feder M, Bujnicki JM. Phylogenomic analysis of the GIY-YIG nuclease superfamily.. 2006. BMC Genomics, 7 98. details
  • Cymerman IA, Obarska A, Skowronek KJ, Lubys A, Bujnicki JM. Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease. 2006. Proteins, 65 867-76. details
  • Chiang PK, Bujnicki JM, Su X, Lanar DE. Malaria: therapy, genes and vaccines.. 2006. Curr Mol Med, 6 309-26. details
  • Carpenter M, Divvela P, Pingoud V, Bujnicki J, Bhagwat AS. Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI.. 2006. Nucleic Acids Res, 34 3762-70. details
  • Bujnicki JM. Protein-structure prediction by recombination of fragments.. 2006. Chembiochem, 7 19-27. details
  • Bheemanaik S, Bujnicki JM, Nagaraja V, Rao DN. Functional analysis of amino acid residues at the dimerisation interface of KpnI DNA methyltransferase.. 2006. Biol Chem, 387 515-23. details
  • Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM. MODOMICS: a database of RNA modification pathways.. 2006. Nucleic Acids Res, 34 D145-9. details
  • 2005
  • Radlińska M, Piekarowicz A, Galimand M, Bujnicki JM. Cloning and preliminary characterization of a GATC-specific beta2-class DNA:m6A methyltransferase encoded by transposon Tn1549 from Enterococcus spp.. 2005. Pol J Microbiol, 54 249-52. details
  • Radlinska M, Kondrzycka-Dada A, Piekarowicz A, Bujnicki JM. Identification of amino acids important for target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine-scanning mutagenesis of residues at the protein-DNA interface.. 2005. Proteins, 58 263-70. details
  • Raczko AM, Bujnicki JM, Pawlowski M, Godlewska R, Lewandowska M, Jagusztyn-Krynicka EK. Characterization of new DsbB-like thiol-oxidoreductases of Campylobacter jejuni and Helicobacter pylori and classification of the DsbB family based on phylogenomic, structural and functional criteria.. 2005. Microbiology, 151 219-31. details
  • Purushothaman SK, Bujnicki JM, Grosjean H, Lapeyre B. Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA.. 2005. Mol Cell Biol, 25 4359-70. details
  • Kosinski J, Steindorf I, Bujnicki JM, Giron-Monzon L, Friedhoff P. Analysis of the quaternary structure of the MutL C-terminal domain.. 2005. J Mol Biol, 351 895-909. details
  • Kosinski J, Gajda MJ, Cymerman IA, Kurowski MA, Pawlowski M, Boniecki M, Obarska A, Papaj G, Sroczynska-Obuchowicz P, Tkaczuk KL, Sniezynska P, Sasin JM, Augustyn A, Bujnicki JM, Feder M. FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6.. 2005. Proteins, 61 Suppl 7 106-13. details
  • Tkaczuk KL, Bujnicki JM, Bialkowska A, Bielecki S, Turkiewicz M, Cieslinski H, Kur J. Molecular modeling of a psychrophilic β-galactosidase. 2005. Biocatal Biotransform, 23 201-209. details
  • Radlińska M, Piekarowicz A, Galimand M, Bujnicki JM. Cloning and preliminary characterization of a GATC-specific beta2-class DNA:m6A methyltransferase encoded by transposon Tn1549 from Enterococcus spp.. 2005. Pol J Microbiol, 54 249-52. details
  • Radlinska M, Kondrzycka-Dada A, Piekarowicz A, Bujnicki JM. Identification of amino acids important for target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine-scanning mutagenesis of residues at the protein-DNA interface.. 2005. Proteins, 58 263-70. details
  • Raczko AM, Bujnicki JM, Pawlowski M, Godlewska R, Lewandowska M, Jagusztyn-Krynicka EK. Characterization of new DsbB-like thiol-oxidoreductases of Campylobacter jejuni and Helicobacter pylori and classification of the DsbB family based on phylogenomic, structural and functional criteria.. 2005. Microbiology, 151 219-31. details
  • Purta E, van Vliet F, Tricot C, De Bie LG, Feder M, Skowronek K, Droogmans L, Bujnicki JM. Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis.. 2005. Proteins, 59 482-8. details
  • Purushothaman SK, Bujnicki JM, Grosjean H, Lapeyre B. Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA.. 2005. Mol Cell Biol, 25 4359-70. details
  • Pingoud V, Sudina A, Geyer H, Bujnicki JM, Lurz R, Lüder G, Morgan R, Kubareva E, Pingoud A. Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences. 2005. J Biol Chem, 280 4289-98. details
  • Pingoud V, Geyer H, Geyer R, Kubareva E, Bujnicki JM, Pingoud A. Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII. 2005. Mol Biosyst, 1 135-41. details
  • Pawlak SD, Radlinska M, Chmiel AA, Bujnicki JM, Skowronek KJ. Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII. 2005. Nucleic Acids Res, 33 661-71. details
  • Kosinski J, Steindorf I, Bujnicki JM, Giron-Monzon L, Friedhoff P. Analysis of the quaternary structure of the MutL C-terminal domain.. 2005. J Mol Biol, 351 895-909. details
  • Kosinski J, Feder M, Bujnicki JM. The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function.. 2005. BMC Bioinformatics, 6 172. details
  • Koliński A, Bujnicki JM. Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.. 2005. Proteins, 61 Suppl 7 84-90. details
  • Ishikawa K, Watanabe M, Kuroita T, Uchiyama I, Bujnicki JM, Kawakami B, Tanokura M, Kobayashi I. Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi. 2005. Nucleic Acids Res, 33 e112. details
  • Feder M, Bujnicki JM. Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site.. 2005. BMC Genomics, 6 21. details
  • Cymerman IA, Meiss G, Bujnicki JM. DNase II is a member of the phospholipase D superfamily.. 2005. Bioinformatics, 21 3959-62. details
  • Chmiel AA, Radlinska M, Pawlak SD, Krowarsch D, Bujnicki JM, Skowronek KJ. A theoretical model of restriction endonuclease NlaIV in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis and circular dichroism spectroscopy.. 2005. Protein Eng Des Sel, 18 181-9. details
  • Chmiel AA, Bujnicki JM, Skowronek KJ. A homology model of restriction endonuclease SfiI in complex with DNA. 2005. BMC Struct Biol, 5 2. details
  • Bujnicki J.M.. Przewidywanie struktury bialek: Boltzmann i Darwin. 2005. Kosmos, 2-3 000-000. details
  • Armalyte E, Bujnicki JM, Giedriene J, Gasiunas G, Kosiński J, Lubys A. Mva1269I: a monomeric type IIS restriction endonuclease from Micrococcus varians with two EcoRI- and FokI-like catalytic domains.. 2005. J Biol Chem, 280 41584-94. details
  • 2004
  • Ye X, O\'Neil PK, Foster AN, Gajda MJ, Kosinski J, Kurowski MA, Bujnicki JM, Friedman AM, Bailey-Kellogg C. Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure.. 2004. Protein Sci, 13 3298-313. details
  • Schäfer P, Scholz SR, Gimadutdinow O, Cymerman IA, Bujnicki JM, Ruiz-Carrillo A, Pingoud A, Meiss G. Structural and functional characterization of mitochondrial EndoG, a sugar non-specific nuclease which plays an important role during apoptosis.. 2004. J Mol Biol, 338 217-28. details
  • Sasin JM, Bujnicki JM. COLORADO3D, a web server for the visual analysis of protein structures.. 2004. Nucleic Acids Res, 32 W586-9. details
  • Saravanan M, Bujnicki JM, Cymerman IA, Rao DN, Nagaraja V. Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily.. 2004. Nucleic Acids Res, 32 6129-35. details
  • Roovers M, Wouters J, Bujnicki JM, Tricot C, Stalon V, Grosjean H, Droogmans L. A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. 2004. Nucleic Acids Res, 32 465-76. details
  • Potluri S, Khan AA, Kuzminykh A, Bujnicki JM, Friedman AM, Bailey-Kellogg C. Geometric analysis of cross-linkability for protein fold discrimination.. 2004. Pac Symp Biocomput, 447-58. details
  • Paziewska A, Wyrwicz LS, Bujnicki JM, Bomsztyk K, Ostrowski J. Cooperative binding of the hnRNP K three KH domains to mRNA targets.. 2004. FEBS Lett, 577 134-40. details
  • Nes WD, Jayasimha P, Zhou W, Kanagasabai R, Jin C, Jaradat TT, Shaw RW, Bujnicki JM. Sterol methyltransferase: functional analysis of highly conserved residues by site-directed mutagenesis.. 2004. Biochemistry, 43 569-76. details
  • Maravić G, Bujnicki JM, Flögel M. Mutational analysis of basic residues in the N-terminus of the rRNA:m6A methyltransferase ErmC'. 2004. Folia Microbiol (Praha), 49 3-7. details
  • Koudan EV, Bujnicki JM, Gromova ES. Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy.. 2004. J Biomol Struct Dyn, 22 339-45. details
  • Bujnicki JM, Oudjama Y, Roovers M, Owczarek S, Caillet J, Droogmans L. Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA.. 2004. RNA, 10 1236-42. details
  • Bujnicki JM, Feder M, Ayres CL, Redman KL. Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases.. 2004. Nucleic Acids Res, 32 2453-63. details
  • Armengaud J, Urbonavicius J, Fernandez B, Chaussinand G, Bujnicki JM, Grosjean H. N2-methylation of guanosine at position 10 in tRNA is catalyzed by a THUMP domain-containing, S-adenosylmethionine-dependent methyltransferase, conserved in Archaea and Eukaryota.. 2004. J Biol Chem, 279 37142-52. details
  • Koudan EV, Bujnicki JM, Gromova ES. Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy.. 2004. J Biomol Struct Dyn, 22 339-45. details
  • Bujnicki JM, Oudjama Y, Roovers M, Owczarek S, Caillet J, Droogmans L. Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA.. 2004. RNA, 10 1236-42. details
  • Bujnicki JM, Feder M, Ayres CL, Redman KL. Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases.. 2004. Nucleic Acids Res, 32 2453-63. details
  • Armengaud J, Urbonavicius J, Fernandez B, Chaussinand G, Bujnicki JM, Grosjean H. N2-methylation of guanosine at position 10 in tRNA is catalyzed by a THUMP domain-containing, S-adenosylmethionine-dependent methyltransferase, conserved in Archaea and Eukaryota.. 2004. J Biol Chem, 279 37142-52. details
  • 2003
  • Scholz SR, Korn C, Bujnicki JM, Gimadutdinow O, Pingoud A, Meiss G. Experimental evidence for a beta beta alpha-Me-finger nuclease motif to represent the active site of the caspase-activated DNase.. 2003. Biochemistry, 42 9288-94. details
  • Sasin JM, Kurowski MA, Bujnicki JM. STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification.. 2003. Bioinformatics, 19 Suppl 1 i252-4. details
  • Pingoud V, Conzelmann C, Kinzebach S, Sudina A, Metelev V, Kubareva E, Bujnicki JM, Lurz R, Lüder G, Xu SY, Pingoud A. PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes. 2003. J Mol Biol, 329 913-29. details
  • Mouaikel J, Bujnicki JM, Tazi J, Bordonné R. Sequence-structure-function relationships of Tgs1, the yeast snRNA/snoRNA cap hypermethylase. 2003. Nucleic Acids Res, 31 4899-909. details
  • Maravić G, Feder M, Pongor S, Flögel M, Bujnicki JM. Mutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC'. 2003. J Mol Biol, 332 99-109. details
  • Maravić G, Bujnicki JM, Feder M, Pongor S, Flögel M. Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions. 2003. Nucleic Acids Res, 31 4941-9. details
  • Kurowski MA, Sasin JM, Feder M, Debski J, Bujnicki JM. Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures.. 2003. BMC Bioinformatics, 4 9. details
  • Kurowski MA, Bujnicki JM. GeneSilico protein structure prediction meta-server.. 2003. Nucleic Acids Res, 31 3305-7. details
  • Kurowski MA, Bhagwat AS, Papaj G, Bujnicki JM. Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB.. 2003. BMC Genomics, 4 48. details
  • Kosinski J, Cymerman IA, Feder M, Kurowski MA, Sasin JM, Bujnicki JM. A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation. 2003. Proteins, 53 Suppl 6 369-79. details
  • Gordon RK, Ginalski K, Rudnicki WR, Rychlewski L, Pankaskie MC, Bujnicki JM, Chiang PK. Anti-HIV-1 activity of 3-deaza-adenosine analogs. Inhibition of S-adenosylhomocysteine hydrolase and nucleotide congeners.. 2003. Eur J Biochem, 270 3507-17. details
  • Feder M, Pas J, Wyrwicz LS, Bujnicki JM. Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases. 2003. Gene, 302 129-38. details
  • Droogmans L, Roovers M, Bujnicki JM, Tricot C, Hartsch T, Stalon V, Grosjean H. Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures.. 2003. Nucleic Acids Res, 31 2148-56. details
  • De Bie LG, Roovers M, Oudjama Y, Wattiez R, Tricot C, Stalon V, Droogmans L, Bujnicki JM. The yggH gene of Escherichia coli encodes a tRNA (m7G46) methyltransferase.. 2003. J Bacteriol, 185 3238-43. details
  • Bujnicki JM, Prigge ST, Caridha D, Chiang PK. Structure, evolution, and inhibitor interaction of S-adenosyl-L-homocysteine hydrolase from Plasmodium falciparum.. 2003. Proteins, 52 624-32. details
  • Bujnicki JM, Albert MA, Nelson DJ, Thurlow DL. Fold recognition, homology modeling, docking simulations, kinetics analysis and mutagenesis of ATP/CTP:tRNA nucleotidyltransferase from Methanococcus jannaschii.. 2003. Proteins, 52 349-59. details
  • Bujnicki JM. Crystallographic and bioinformatic studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology. 2003. Curr Protein Pept Sci, 4 327-37. details
  • Coker JA, Sheridan PP, Loveland-Curtze J, Gutshall KR, Auman AJ, Brenchley JE. Biochemical characterization of a beta-galactosidase with a low temperature optimum obtained from an Antarctic arthrobacter isolate.. 2003. J Bacteriol, 185 5473-82. details
  • Coker JA, Sheridan PP, Loveland-Curtze J, Gutshall KR, Auman AJ, Brenchley JE. Biochemical characterization of a beta-galactosidase with a low temperature optimum obtained from an Antarctic arthrobacter isolate.. 2003. J Bacteriol, 185 5473-82. details
  • 2002
  • Zhang P, Nicholson DE, Bujnicki JM, Su X, Brendle JJ, Ferdig M, Kyle DE, Milhous WK, Chiang PK. Angiogenesis inhibitors specific for methionine aminopeptidase 2 as drugs for malaria and leishmaniasis. 2002. J Biomed Sci, 9 34-40. details
  • Xu Y, Keene DR, Bujnicki JM, Höök M, Lukomski S. Streptococcal Scl1 and Scl2 proteins form collagen-like triple helices.. 2002. J Biol Chem, 277 27312-8. details
  • Pintard L, Lecointe F, Bujnicki JM, Bonnerot C, Grosjean H, Lapeyre B. Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop. 2002. EMBO J, 21 1811-20. details
  • Pintard L, Bujnicki JM, Lapeyre B, Bonnerot C. MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase. 2002. EMBO J, 21 1139-47. details
  • Pingoud V, Kubareva E, Stengel G, Friedhoff P, Bujnicki JM, Urbanke C, Sudina A, Pingoud A. Evolutionary relationship between different subgroups of restriction endonucleases.. 2002. J Biol Chem, 277 14306-14. details
  • Godlewska R, Bujnicki JM, Ostrowski J, Jagusztyn-Krynicka EK. The hppA gene of Helicobacter pylori encodes the class C acid phosphatase precursor. 2002. FEBS Lett, 525 39-42. details
  • Bujnicki J, Rychlewski L, Fischer D. Fold-recognition detects an error in the Protein Data Bank. 2002. Bioinformatics, 18 1391-5. details
  • Bujnicki JM, Rychlewski L. In silico identification, structure prediction and phylogenetic analysis of the 2'-O-ribose (cap 1) methyltransferase domain in the large structural protein of ssRNA negative-strand viruses. 2002. Protein Eng, 15 101-8. details
  • Bujnicki JM, Rychlewski L. RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited--bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure. 2002. BMC Bioinformatics, 3 10. details
  • Bujnicki JM, Rychlewski L. Fold-recognition analysis predicts that the Tag protein family shares a common domain with the helix-hairpin-helix DNA glycosylases. 2002. DNA Repair (Amst), 1 391-5. details
  • Bujnicki JM, Leach RA, Debski J, Rychlewski L. Bioinformatic analyses of the tRNA: (guanine 26, N2,N2)-dimethyltransferase (Trm1) family. 2002. J Mol Microbiol Biotechnol, 4 405-15. details
  • Bujnicki JM, Feder M, Rychlewski L, Fischer D. Errors in the D. radiodurans large ribosomal subunit structure detected by protein fold-recognition and structure validation tools. 2002. FEBS Lett, 525 174-5. details
  • Bujnicki JM, Feder M, Radlinska M, Blumenthal RM. Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA:m(6)A methyltransferase. 2002. J Mol Evol, 55 431-44. details
  • Bujnicki JM, Blumenthal RM, Rychlewski L. Sequence analysis and structure prediction of 23S rRNA:m1G methyltransferases reveals a conserved core augmented with a putative Zn-binding domain in the N-terminus and family-specific elaborations in the C-terminus. 2002. J Mol Microbiol Biotechnol, 4 93-9. details
  • Bujnicki JM. Sequence permutations in the molecular evolution of DNA methyltransferases. 2002. BMC Evol Biol, 2 3. details
  • 2001
  • Radlinska M, Bujnicki JM. Site-directed mutagenesis defines the catalytic aspartate in the active site of the atypical DNA: m4C methyltransferase M.NgoMXV. 2001. Acta Microbiol Pol, 50 97-105. details
  • Radlinska M, Bujnicki JM. Cloning of enterohemorrhagic Escherichia coli phage VT-2 dam methyltransferase. 2001. Acta Microbiol Pol, 50 161-7. details
  • Lundström J, Rychlewski L, Bujnicki J, Elofsson A. Pcons: a neural-network-based consensus predictor that improves fold recognition. 2001. Protein Sci, 10 2354-62. details
  • Bujnicki JM, Rychlewski L. The herpesvirus alkaline exonuclease belongs to the restriction endonuclease PD-(D/E)XK superfamily: insight from molecular modeling and phylogenetic analysis.. 2001. Virus Genes, 22 219-30. details
  • Bujnicki JM, Rychlewski L. Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles.. 2001. J Mol Microbiol Biotechnol, 3 69-72. details
  • Bujnicki JM, Rychlewski L. Reassignment of specificities of two cap methyltransferase domains in the reovirus lambda 2 protein. 2001. Genome Biol, 2 RESEARCH0038. details
  • Bujnicki JM, Rychlewski L. Unusual evolutionary history of the tRNA splicing endonuclease EndA: relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases.. 2001. Protein Sci, 10 656-60. details
  • Bujnicki JM, Rychlewski L. Identification of a PD-(D/E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs. 2001. Gene, 267 183-91. details
  • Bujnicki JM, Rychlewski L. Sequence analysis and structure prediction of aminoglycoside-resistance 16S rRNA:m7G methyltransferases. 2001. Acta Microbiol Pol, 50 7-17. details
  • Bujnicki JM, Rotkiewicz P, Kolinski A, Rychlewski L. Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics.. 2001. Protein Eng, 14 717-21. details
  • Bujnicki JM, Radlinska M, Zaleski P, Piekarowicz A. Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage. 2001. Acta Biochim Pol, 48 969-83. details
  • Bujnicki JM, Radlinska M, Rychlewski L. Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed. 2001. Trends Biochem Sci, 26 9-11. details
  • Bujnicki JM, Radlinska M. Cloning and characterization of M.LmoA118I, a novel DNA:m4C methyltransferase from the Listeria monocytogenes phage A118, a close homolog of M.NgoMXV. 2001. Acta Microbiol Pol, 50 155-60. details
  • Bujnicki JM, Feder M, Radlinska M, Rychlewski L. mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships. 2001. BMC Bioinformatics, 2 2. details
  • Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. LiveBench-2: large-scale automated evaluation of protein structure prediction servers.. 2001. Proteins, Suppl 5 184-91. details
  • Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. LiveBench-1: continuous benchmarking of protein structure prediction servers. 2001. Protein Sci, 10 352-61. details
  • Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. Structure prediction meta server. 2001. Bioinformatics, 17 750-1. details
  • Bujnicki JM. A model of structure and action of Sau3AI restriction endonuclease that comprises two MutH-like endonuclease domains within a single polypeptide.. 2001. Acta Microbiol Pol, 50 219-31. details
  • Bujnicki JM. Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons.. 2001. Acta Biochim Pol, 48 935-67. details
  • Bujnicki JM. In silico analysis of the tRNA:m1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea. 2001. FEBS Lett, 507 123-7. details
  • 2000
  • Bujnicki JM, Rychlewski L. Prediction of a common fold for all four subunits of the yeast tRNA splicing endonuclease: implications for the evolution of the EndA/Sen family.. 2000. FEBS Lett, 486 328-9. details
  • Bujnicki JM, Rychlewski L. Prediction of a novel RNA 2'-O-ribose methyltransferase subfamily encoded by the Escherichia coli YgdE open reading frame and its orthologs. 2000. Acta Microbiol Pol, 49 253-60. details
  • Bujnicki JM, Radlinska M, Rychlewski L. Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc finger and structural similarity to betabetaalphaMe endonucleases. 2000. Mol Microbiol, 37 1280-1. details
  • Bujnicki JM. Sequence, structural, and evolutionary analysis of prokaryotic ribosomal protein L11 methyltransferases.. 2000. Acta Microbiol Pol, 49 19-29. details
  • Bujnicki JM. Phylogenomic analysis of 16S rRNA:(guanine-N2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino-methyltransferases.. 2000. FASEB J, 14 2365-8. details