Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures. Kurowski MA, Sasin JM, Feder M, Debski J, Bujnicki JM BMC Bioinformatics. 2003 GeneSilico protein structure prediction meta-server. Kurowski MA, Bujnicki JM Nucleic Acids Res. 2003 Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB. Kurowski MA, Bhagwat AS, Papaj G, Bujnicki JM BMC Genomics. 2003 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 Kosinski J, Cymerman IA, Feder M, Kurowski MA, Sasin JM, Bujnicki JM Proteins. 2003 Anti-HIV-1 activity of 3-deaza-adenosine analogs. Inhibition of S-adenosylhomocysteine hydrolase and nucleotide congeners. Gordon RK, Ginalski K, Rudnicki WR, Rychlewski L, Pankaskie MC, Bujnicki JM, Chiang PK Eur J Biochem. 2003 Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases Feder M, Pas J, Wyrwicz LS, Bujnicki JM Gene. 2003 Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures. Droogmans L, Roovers M, Bujnicki JM, Tricot C, Hartsch T, Stalon V, Grosjean H Nucleic Acids Res. 2003 The yggH gene of Escherichia coli encodes a tRNA (m7G46) methyltransferase. De Bie LG, Roovers M, Oudjama Y, Wattiez R, Tricot C, Stalon V, Droogmans L, Bujnicki JM J Bacteriol. 2003 Structure, evolution, and inhibitor interaction of S-adenosyl-L-homocysteine hydrolase from Plasmodium falciparum. Bujnicki JM, Prigge ST, Caridha D, Chiang PK Proteins. 2003 Fold recognition, homology modeling, docking simulations, kinetics analysis and mutagenesis of ATP/CTP:tRNA nucleotidyltransferase from Methanococcus jannaschii. Bujnicki JM, Albert MA, Nelson DJ, Thurlow DL Proteins. 2003 Crystallographic and bioinformatic studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology Bujnicki JM Curr Protein Pept Sci. 2003 Angiogenesis inhibitors specific for methionine aminopeptidase 2 as drugs for malaria and leishmaniasis Zhang P, Nicholson DE, Bujnicki JM, Su X, Brendle JJ, Ferdig M, Kyle DE, Milhous WK, Chiang PK J Biomed Sci. 2002 Streptococcal Scl1 and Scl2 proteins form collagen-like triple helices. Xu Y, Keene DR, Bujnicki JM, Höök M, Lukomski S J Biol Chem. 2002 Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop Pintard L, Lecointe F, Bujnicki JM, Bonnerot C, Grosjean H, Lapeyre B EMBO J. 2002 MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase Pintard L, Bujnicki JM, Lapeyre B, Bonnerot C EMBO J. 2002 Evolutionary relationship between different subgroups of restriction endonucleases. Pingoud V, Kubareva E, Stengel G, Friedhoff P, Bujnicki JM, Urbanke C, Sudina A, Pingoud A J Biol Chem. 2002 The hppA gene of Helicobacter pylori encodes the class C acid phosphatase precursor Godlewska R, Bujnicki JM, Ostrowski J, Jagusztyn-Krynicka EK FEBS Lett. 2002 Fold-recognition detects an error in the Protein Data Bank Bujnicki J, Rychlewski L, Fischer D Bioinformatics. 2002 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 Bujnicki JM, Rychlewski L Protein Eng. 2002 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 Bujnicki JM, Rychlewski L BMC Bioinformatics. 2002 Fold-recognition analysis predicts that the Tag protein family shares a common domain with the helix-hairpin-helix DNA glycosylases Bujnicki JM, Rychlewski L DNA Repair (Amst). 2002 Bioinformatic analyses of the tRNA: (guanine 26, N2,N2)-dimethyltransferase (Trm1) family Bujnicki JM, Leach RA, Debski J, Rychlewski L J Mol Microbiol Biotechnol. 2002 Errors in the D. radiodurans large ribosomal subunit structure detected by protein fold-recognition and structure validation tools Bujnicki JM, Feder M, Rychlewski L, Fischer D FEBS Lett. 2002 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 Bujnicki JM, Feder M, Radlinska M, Blumenthal RM J Mol Evol. 2002 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 Bujnicki JM, Blumenthal RM, Rychlewski L J Mol Microbiol Biotechnol. 2002 Sequence permutations in the molecular evolution of DNA methyltransferases Bujnicki JM BMC Evol Biol. 2002 Site-directed mutagenesis defines the catalytic aspartate in the active site of the atypical DNA: m4C methyltransferase M.NgoMXV Radlinska M, Bujnicki JM Acta Microbiol Pol. 2001 Cloning of enterohemorrhagic Escherichia coli phage VT-2 dam methyltransferase Radlinska M, Bujnicki JM Acta Microbiol Pol. 2001 Pcons: a neural-network-based consensus predictor that improves fold recognition Lundström J, Rychlewski L, Bujnicki J, Elofsson A Protein Sci. 2001 The herpesvirus alkaline exonuclease belongs to the restriction endonuclease PD-(D/E)XK superfamily: insight from molecular modeling and phylogenetic analysis. Bujnicki JM, Rychlewski L Virus Genes. 2001