Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis. Skowronek KJ, Kosinski J, Bujnicki JM Proteins. 2006 Curcumin induces caspase-3-dependent apoptotic pathway but inhibits DNA fragmentation factor 40/caspase-activated DNase endonuclease in human Jurkat cells. Sikora E, Bielak-Zmijewska A, Magalska A, Piwocka K, Mosieniak G, Kalinowska M, Widlak P, Cymerman IA, Bujnicki JM Mol Cancer Ther. 2006 Evaluation of molecular models for the affinity maturation of antibodies: roles of cytosine deamination by AID and DNA repair. Samaranayake M, Bujnicki JM, Carpenter M, Bhagwat AS Chem Rev. 2006 The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase. Purta E, van Vliet F, Tkaczuk KL, Dunin-Horkawicz S, Mori H, Droogmans L, Bujnicki JM BMC Mol Biol. 2006 Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA. Obarska A, Blundell A, Feder M, Vejsadová S, Sisáková E, Weiserová M, Bujnicki JM, Firman K Nucleic Acids Res. 2006 Casein kinases phosphorylate multiple residues spanning the entire hnRNP K length. Mikula M, Karczmarski J, Dzwonek A, Rubel T, Hennig E, Dadlez M, Bujnicki JM, Bomsztyk K, Ostrowski J Biochim Biophys Acta. 2006 The yeast Arr4p ATPase binds the chloride transporter Gef1p when copper is available in the cytosol. Metz J, Wächter A, Schmidt B, Bujnicki JM, Schwappach B J Biol Chem. 2006 Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa. Klimek-Tomczak K, Mikula M, Dzwonek A, Paziewska A, Karczmarski J, Hennig E, Bujnicki JM, Bragoszewski P, Denisenko O, Bomsztyk K, Ostrowski J Br J Cancer. 2006 Binding of the low-density lipoprotein by streptococcal collagen-like protein Scl1 of Streptococcus pyogenes. Han R, Caswell CC, Lukomska E, Keene DR, Pawlowski M, Bujnicki JM, Kim JK, Lukomski S Mol Microbiol. 2006 Characterization of prmt7alpha and beta isozymes from Chinese hamster cells sensitive and resistant to topoisomerase II inhibitors. Gros L, Renodon-Cornière A, de Saint Vincent BR, Feder M, Bujnicki JM, Jacquemin-Sablon A Biochim Biophys Acta. 2006 Helicobacter pylori protein oxidation influences the colonization process. Godlewska R, Dzwonek A, Mikuła M, Ostrowski J, Pawłowski M, Bujnicki JM, Jagusztyn-Krynicka EK Int J Med Microbiol. 2006 THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain. 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 Nucleic Acids Res. 2006 Phylogenomic analysis of the GIY-YIG nuclease superfamily. Dunin-Horkawicz S, Feder M, Bujnicki JM BMC Genomics. 2006 Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease Cymerman IA, Obarska A, Skowronek KJ, Lubys A, Bujnicki JM Proteins. 2006 Malaria: therapy, genes and vaccines. Chiang PK, Bujnicki JM, Su X, Lanar DE Curr Mol Med. 2006 Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI. Carpenter M, Divvela P, Pingoud V, Bujnicki J, Bhagwat AS Nucleic Acids Res. 2006 Protein-structure prediction by recombination of fragments. Bujnicki JM Chembiochem. 2006 Functional analysis of amino acid residues at the dimerisation interface of KpnI DNA methyltransferase. Bheemanaik S, Bujnicki JM, Nagaraja V, Rao DN Biol Chem. 2006 MODOMICS: a database of RNA modification pathways. Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM Nucleic Acids Res. 2006 Cloning and preliminary characterization of a GATC-specific beta2-class DNA:m6A methyltransferase encoded by transposon Tn1549 from Enterococcus spp. Radlińska M, Piekarowicz A, Galimand M, Bujnicki JM Pol J Microbiol. 2005 Analysis of the quaternary structure of the MutL C-terminal domain. Kosinski J, Steindorf I, Bujnicki JM, Giron-Monzon L, Friedhoff P J Mol Biol. 2005 FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6. 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 Proteins. 2005 Molecular modeling of a psychrophilic β-galactosidase Tkaczuk KL, Bujnicki JM, Bialkowska A, Bielecki S, Turkiewicz M, Cieslinski H, Kur J Biocatal Biotransform. 2005 Publication 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. Radlinska M, Kondrzycka-Dada A, Piekarowicz A, Bujnicki JM. Proteins. 2005 Publication 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. Raczko AM, Bujnicki JM, Pawlowski M, Godlewska R, Lewandowska M, Jagusztyn-Krynicka EK Microbiology. 2005 Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis. Purta E, van Vliet F, Tricot C, De Bie LG, Feder M, Skowronek K, Droogmans L, Bujnicki JM Proteins. 2005 Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA. Purushothaman SK, Bujnicki JM, Grosjean H, Lapeyre B. Mol Cell Biol. 2005 Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences Pingoud V, Sudina A, Geyer H, Bujnicki JM, Lurz R, Lüder G, Morgan R, Kubareva E, Pingoud A J Biol Chem. 2005 Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII Pingoud V, Geyer H, Geyer R, Kubareva E, Bujnicki JM, Pingoud A Mol Biosyst. 2005 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 Pawlak SD, Radlinska M, Chmiel AA, Bujnicki JM, Skowronek KJ Nucleic Acids Res. 2005