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 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. Kosinski J, Feder M, Bujnicki JM BMC Bioinformatics. 2005 Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. Koliński A, Bujnicki JM Proteins. 2005 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 Ishikawa K, Watanabe M, Kuroita T, Uchiyama I, Bujnicki JM, Kawakami B, Tanokura M, Kobayashi I Nucleic Acids Res. 2005 Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site. Feder M, Bujnicki JM BMC Genomics. 2005 DNase II is a member of the phospholipase D superfamily. Cymerman IA, Meiss G, Bujnicki JM Bioinformatics. 2005 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. Chmiel AA, Radlinska M, Pawlak SD, Krowarsch D, Bujnicki JM, Skowronek KJ Protein Eng Des Sel. 2005 A homology model of restriction endonuclease SfiI in complex with DNA Chmiel AA, Bujnicki JM, Skowronek KJ BMC Struct Biol. 2005 Przewidywanie struktury bialek: Boltzmann i Darwin Bujnicki J.M. Kosmos. 2005 Mva1269I: a monomeric type IIS restriction endonuclease from Micrococcus varians with two EcoRI- and FokI-like catalytic domains. Armalyte E, Bujnicki JM, Giedriene J, Gasiunas G, Kosiński J, Lubys A J Biol Chem. 2005 Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure. Ye X, O\'Neil PK, Foster AN, Gajda MJ, Kosinski J, Kurowski MA, Bujnicki JM, Friedman AM, Bailey-Kellogg C Protein Sci. 2004 Structural and functional characterization of mitochondrial EndoG, a sugar non-specific nuclease which plays an important role during apoptosis. Schäfer P, Scholz SR, Gimadutdinow O, Cymerman IA, Bujnicki JM, Ruiz-Carrillo A, Pingoud A, Meiss G J Mol Biol. 2004 COLORADO3D, a web server for the visual analysis of protein structures. Sasin JM, Bujnicki JM Nucleic Acids Res. 2004 Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily. Saravanan M, Bujnicki JM, Cymerman IA, Rao DN, Nagaraja V Nucleic Acids Res. 2004 A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase Roovers M, Wouters J, Bujnicki JM, Tricot C, Stalon V, Grosjean H, Droogmans L Nucleic Acids Res. 2004 Geometric analysis of cross-linkability for protein fold discrimination. Potluri S, Khan AA, Kuzminykh A, Bujnicki JM, Friedman AM, Bailey-Kellogg C Pac Symp Biocomput. 2004 Cooperative binding of the hnRNP K three KH domains to mRNA targets. Paziewska A, Wyrwicz LS, Bujnicki JM, Bomsztyk K, Ostrowski J FEBS Lett. 2004 Sterol methyltransferase: functional analysis of highly conserved residues by site-directed mutagenesis. Nes WD, Jayasimha P, Zhou W, Kanagasabai R, Jin C, Jaradat TT, Shaw RW, Bujnicki JM Biochemistry. 2004 Mutational analysis of basic residues in the N-terminus of the rRNA:m6A methyltransferase ErmC' Maravić G, Bujnicki JM, Flögel M Folia Microbiol (Praha). 2004 Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy. Koudan EV, Bujnicki JM, Gromova ES J Biomol Struct Dyn. 2004 Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy. Koudan EV, Bujnicki JM, Gromova ES J Biomol Struct Dyn. 2004 Publication Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA. Bujnicki JM, Oudjama Y, Roovers M, Owczarek S, Caillet J, Droogmans L. RNA. 2004 Publication Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases. Bujnicki JM, Feder M, Ayres CL, Redman KL Nucleic Acids Res. 2004 Publication 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. Armengaud J, Urbonavicius J, Fernandez B, Chaussinand G, Bujnicki JM, Grosjean H J Biol Chem. 2004 Experimental evidence for a beta beta alpha-Me-finger nuclease motif to represent the active site of the caspase-activated DNase. Scholz SR, Korn C, Bujnicki JM, Gimadutdinow O, Pingoud A, Meiss G Biochemistry. 2003 STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification. Sasin JM, Kurowski MA, Bujnicki JM Bioinformatics. 2003 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 Pingoud V, Conzelmann C, Kinzebach S, Sudina A, Metelev V, Kubareva E, Bujnicki JM, Lurz R, Lüder G, Xu SY, Pingoud A J Mol Biol. 2003 Sequence-structure-function relationships of Tgs1, the yeast snRNA/snoRNA cap hypermethylase Mouaikel J, Bujnicki JM, Tazi J, Bordonné R Nucleic Acids Res. 2003 Mutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC' Maravić G, Feder M, Pongor S, Flögel M, Bujnicki JM J Mol Biol. 2003 Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions Maravić G, Bujnicki JM, Feder M, Pongor S, Flögel M Nucleic Acids Res. 2003