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Janusz Bujnicki

Research Profile

Concepts & Ideas

Genes & Molecular Sequences

Amino Acid Sequences

Procedures

Sequence Alignment

Chemicals & Drugs

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Kaja Milanowska; Martyna Nowacka; Kristian M Rother; Marcin Skorupski; Zuzanna Balcer; Anna Lukasik; Magdalena A Machnicka; Katarzyna Mikolajczak; Janusz Bujnicki
RNApathwaysDB--a database of RNA maturation and decay pathways.
Magdalena A Machnicka; Kaja Milanowska; Anna Olchowik; Okan Osman Oglou; Elzbieta Purta; Kristian M Rother; Mark Helm; Witold Januszewski; Sebastian Kalinowski; Malgorzata Kurkowska; Janusz Bujnicki; Stanislaw Dunin-Horkawicz; Henri Grosjean
MODOMICS: a database of RNA modification pathways--2013 update.
Agata A Sulej; Irina Tuszynska; Marcin Nowotny; Krzysztof J Skowronek; Janusz Bujnicki
Sequence-specific cleavage of the RNA strand in DNA-RNA hybrids by the fusion of ribonuclease H with a zinc finger.

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All Publications

2013: Kaja Milanowska; Martyna Nowacka; Kristian M Rother; Marcin Skorupski; Zuzanna Balcer; Anna Lukasik; Magdalena A Machnicka; Katarzyna Mikolajczak; Janusz Bujnicki
RNApathwaysDB--a database of RNA maturation and decay pathways.
Nucleic acids research 2013;41(Database issue):D268-72.
2013: Magdalena A Machnicka; Kaja Milanowska; Anna Olchowik; Okan Osman Oglou; Elzbieta Purta; Kristian M Rother; Mark Helm; Witold Januszewski; Sebastian Kalinowski; Malgorzata Kurkowska; Janusz Bujnicki; Stanislaw Dunin-Horkawicz; Henri Grosjean
MODOMICS: a database of RNA modification pathways--2013 update.
Nucleic acids research 2013;41(Database issue):D262-7.
2012: Agata A Sulej; Irina Tuszynska; Marcin Nowotny; Krzysztof J Skowronek; Janusz Bujnicki
Sequence-specific cleavage of the RNA strand in DNA-RNA hybrids by the fusion of ribonuclease H with a zinc finger.
Nucleic acids research 2012;40(22):11563-70.
2012: Wojciech Siwek; Matthias Bochtler; Janusz Bujnicki; Honorata Czapinska; Krzysztof J Skowronek
Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI.
Nucleic acids research 2012;40(15):7563-72.
2012: Iga Korneta; Marcin Magnus; Janusz Bujnicki
Structural bioinformatics of the human spliceosomal proteome.
Nucleic acids research 2012;40(15):7046-65.
2012: Martine Roovers; Wim Versées; Janusz Bujnicki; Marcus Fislage; Yamina Oudjama; Louis Droogmans
The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N²-methylguanosine at position 6 in tRNA.
RNA (New York, N.Y.) 2012;18(4):815-24.
2012: Grzegorz Chojnowski; Janusz Bujnicki; Matthias Bochtler
RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes.
Bioinformatics (Oxford, England) 2012;28(6):880-1.
2012: Marek Drozdz; Andrzej Piekarowicz; Janusz Bujnicki; Monika Radlinska
Novel non-specific DNA adenine methyltransferases.
Nucleic acids research 2012;40(5):2119-30.
2012: Marcin Pawlowski; Janusz Bujnicki
The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement.
BMC bioinformatics 2012;13():289.
2011: Magdalena Rother; Jaroslaw Jeleniewicz; Kaja Milanowska; Tomasz Puton; Kristian Rother; Janusz Bujnicki
ModeRNA server: an online tool for modeling RNA 3D structures.
Bioinformatics (Oxford, England) 2011;27(17):2441-2.
2011: Maria Werner; Jesse R Zamudio; David A Campbell; Iwona A Cymerman; Jacek Jaworski; Katarzyna H Kaminska; Bidyottam Mittra; Elzbieta Purta; Nancy R Sturm; Janusz Bujnicki
2'-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family.
Nucleic acids research 2011;39(11):4756-68.
2011: Nilofer Husain; Sonja Obranic; Lukasz Koscinski; J Seetharaman; Fedora Babic; Janusz Bujnicki; Gordana Maravic-Vlahovicek; J Sivaraman
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.
Nucleic acids research 2011;39(5):1903-18.
2011: Irina Tuszynska; Janusz Bujnicki
DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking.
BMC bioinformatics 2011;12():348.
2011: Kaja Milanowska; Joanna Krwawicz; Grzegorz Papaj; Jan Kosinski; Katarzyna Poleszak; Justyna Lesiak; Ewelina Osinska; Kristian Rother; Janusz Bujnicki
REPAIRtoire--a database of DNA repair pathways.
Nucleic acids research 2011;39(Database issue):D788-92.
2010: Michal J Gajda; Irina Tuszynska; Marta Kaczor; Anastasia Yu Bakulina; Janusz Bujnicki
FILTREST3D: discrimination of structural models using restraints from experimental data.
Bioinformatics (Oxford, England) 2010;26(23):2986-7.
2010: Morgane Kempenaers; Martine Roovers; Yamina Oudjama; Karolina L Tkaczuk; Janusz Bujnicki; Louis Droogmans
New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA.
Nucleic acids research 2010;38(19):6533-43.
2010: Jan Kosinski; Inga Hinrichsen; Janusz Bujnicki; Peter Friedhoff; Guido Plotz
Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair.
Human mutation 2010;31(8):975-82.
2010: Nilofer Husain; Karolina L Tkaczuk; Shenoy Rajesh Tulsidas; Katarzyna H Kaminska; Sonja Cubrilo; Gordana Maravić-Vlahovicek; Janusz Bujnicki; J Sivaraman
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.
Nucleic acids research 2010;38(12):4120-32.
2010: Feroz Khan; Yoshikazu Furuta; Mikihiko Kawai; Katarzyna H Kaminska; Ken Ishikawa; Janusz Bujnicki; Ichizo Kobayashi
A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI).
Nucleic acids research 2010;38(9):3019-30.
2010: Katarzyna H Kaminska; Elzbieta Purta; Lykke H Hansen; Janusz Bujnicki; Birte Vester; Katherine S Long
Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria.
Nucleic acids research 2010;38(5):1652-63.
2010: Irina Tuszynska; Janusz Bujnicki
Predicting atomic details of the unfolding pathway for YibK, a knotted protein from the SPOUT superfamily.
Journal of biomolecular structure & dynamics 2010;27(4):511-20.
2009: Tomasz A Leski; Clayton C Caswell; Marcin Pawlowski; David J Klinke; Janusz Bujnicki; Sean J Hart; Slawomir Lukomski
Identification and classification of bcl genes and proteins of Bacillus cereus group organisms and their application in Bacillus anthracis detection and fingerprinting.
Applied and environmental microbiology 2009;75(22):7163-72.
2009: Elzbieta Purta; Michelle O'Connor; Janusz Bujnicki; Stephen Douthwaite
YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA.
Molecular microbiology 2009;72(5):1147-58.
2009: Karolina A Majorek; Janusz Bujnicki
Modeling of Escherichia coli Endonuclease V structure in complex with DNA.
Journal of molecular modeling 2009;15(2):173-82.
2009: Marcin Pawłowski; Anna M Lasica; Elzbieta K Jagusztyn-Krynicka; Janusz Bujnicki
AAN82231 protein from uropathogenic E. coli CFT073 is a close paralog of DsbB enzymes and does not belong to the DsbI family.
Polish journal of microbiology / Polskie Towarzystwo Mikrobiologów = The Polish Society of Microbiologists 2009;58(2):181-4.
2009: Joanna Nakonieczna; Tadeusz Kaczorowski; Agnieszka Obarska-Kosinska; Janusz Bujnicki
Functional analysis of MmeI from methanol utilizer Methylophilus methylotrophus, a subtype IIC restriction-modification enzyme related to type I enzymes.
Applied and environmental microbiology 2009;75(1):212-23.
2009: Anna Czerwoniec; Stanislaw Dunin-Horkawicz; Elzbieta Purta; Katarzyna H Kaminska; Joanna M Kasprzak; Janusz Bujnicki; Henri Grosjean; Kristian Rother
MODOMICS: a database of RNA modification pathways. 2008 update.
Nucleic acids research 2009;37(Database issue):D118-21.
2008: Jerzy Orlowski; Mehari Tesfazgi Mebrhatu; Chris W Michiels; Janusz Bujnicki; Abram Aertsen
Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr.
Biochemical and biophysical research communications 2008;377(3):862-6.
2008: S Sunita; Karolina L Tkaczuk; Elzbieta Purta; Joanna M Kasprzak; Stephen Douthwaite; Janusz Bujnicki; J Sivaraman
Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes.
Journal of molecular biology 2008;383(3):652-66.
2008: Elzbieta Purta; Michelle O'Connor; Janusz Bujnicki; Stephen Douthwaite
YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962.
Journal of molecular biology 2008;383(3):641-51.
2008: Mads Gyrd-Hansen; Maurice Darding; Maria Miasari; Massimo M Santoro; Lars Zender; Wen Xue; Tencho Tenev; Paula C A da Fonseca; Marketa Zvelebil; Janusz Bujnicki; Scott W Lowe; John Silke; Pascal Meier
IAPs contain an evolutionarily conserved ubiquitin-binding domain that regulates NF-kappaB as well as cell survival and oncogenesis.
Nature cell biology 2008;10(11):1309-17.
2008: Jan Kosinski; Guido Plotz; Alba Guarné; Janusz Bujnicki; Peter Friedhoff
The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family.
Journal of molecular biology 2008;382(3):610-27.
2008: Elzbieta Purta; Katarzyna H Kaminska; Joanna M Kasprzak; Janusz Bujnicki; Stephen Douthwaite
YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA.
RNA (New York, N.Y.) 2008;14(10):2234-44.
2008: Jerzy Orlowski; Janusz Bujnicki
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.
Nucleic acids research 2008;36(11):3552-69.
2008: Martine Roovers; Katarzyna H Kaminska; Karolina L Tkaczuk; Daniel Gigot; Louis Droogmans; Janusz Bujnicki
The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK).
Nucleic acids research 2008;36(10):3252-62.
2008: Martine Roovers; Yamina Oudjama; Katarzyna H Kaminska; Elzbieta Purta; Joël Caillet; Louis Droogmans; Janusz Bujnicki
Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA.
Proteins 2008;71(4):2076-85.
2008: Joshua White; Zhihua Li; Richa Sardana; Janusz Bujnicki; Edward M Marcotte; Arlen W Johnson
Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits.
Molecular and cellular biology 2008;28(10):3151-61.
2008: Teck Khiang Chua; Janusz Bujnicki; Tien-Chye Tan; Frederick Huynh; Bharat K. C. Patel; J Sivaraman
The structure of sucrose phosphate synthase from Halothermothrix orenii reveals its mechanism of action and binding mode.
The Plant cell 2008;20(4):1059-72.
2008: Gordana Maravić Vlahovicek; Sonja Cubrilo; Karolina L Tkaczuk; Janusz Bujnicki
Modeling and experimental analyses reveal a two-domain structure and amino acids important for the activity of aminoglycoside resistance methyltransferase Sgm.
Biochimica et biophysica acta 2008;1784(4):582-90.
2008: Taner Z Sen; Margaret Kloster; Robert L Jernigan; Andrzej Kolinski; Janusz Bujnicki; Andrzej Kloczkowski
Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA.
Biophysical journal 2008;94(7):2482-91.
2008: Iwona A Cymerman; Inn Chung; Benedikt M Beckmann; Janusz Bujnicki; Gregor Meiss
EXOG, a novel paralog of Endonuclease G in higher eukaryotes.
Nucleic acids research 2008;36(4):1369-79.
2008: Ashok S Bhagwat; Michael A Carpenter; Janusz Bujnicki
Is AID a monomer in solution?
DNA repair 2008;7(3):349-50; author reply 351-2.
2008: Agnieszka Obarska-Kosinska; James E Taylor; Philip Callow; Jerzy Orlowski; Janusz Bujnicki; G Geoff Kneale
HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling.
Journal of molecular biology 2008;376(2):438-52.
2008: Bidyottam Mittra; Jesse R Zamudio; Janusz Bujnicki; Janusz Stepinski; Edward Darzynkiewicz; David A Campbell; Nancy R Sturm
The TbMTr1 spliced leader RNA cap 1 2'-O-ribose methyltransferase from Trypanosoma brucei acts with substrate specificity.
The Journal of biological chemistry 2008;283(6):3161-72.
2008: Kommireddy Vasu; Matheshwaran Saravanan; Janusz Bujnicki; Valakunja Nagaraja
Structural integrity of the beta beta alpha-Metal finger motif is required for DNA binding and stable protein-DNA complex formation in R.KpnI.
Biochimica et biophysica acta 2008;1784(2):269-75.
2008: Marcin Feder; Elzbieta Purta; Lukasz Koscinski; Sonja Cubrilo; Gordana Maravic Vlahovicek; Janusz Bujnicki
Virtual screening and experimental verification to identify potential inhibitors of the ErmC methyltransferase responsible for bacterial resistance against macrolide antibiotics.
ChemMedChem 2008;3(2):316-22.
2008: Eri Fukuda; Katarzyna H Kaminska; Janusz Bujnicki; Ichizo Kobayashi
Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases.
Genome biology 2008;9(11):R163.
2008: Katarzyna H Kaminska; Mikihiko Kawai; Michal Boniecki; Ichizo Kobayashi; Janusz Bujnicki
Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site.
BMC structural biology 2008;8():48.
2008: Marcin Pawlowski; Michal J Gajda; Ryszard Matlak; Janusz Bujnicki
MetaMQAP: a meta-server for the quality assessment of protein models.
BMC bioinformatics 2008;9():403.
2008: Katarzyna H Kaminska; Janusz Bujnicki
Bacteriophage Mu Mom protein responsible for DNA modification is a new member of the acyltransferase superfamily.
Cell cycle (Georgetown, Tex.) 2008;7(1):120-1.
2008: Katarzyna H Kaminska; Urszula Baraniak; Michal Boniecki; Katarzyna Nowaczyk; Anna Czerwoniec; Janusz Bujnicki
Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms(2)io(6)A37 in tRNA.
Proteins 2008;70(1):1-18.
2007: Jacob Sabates Bellver; Laurens G Van der Flier; Mariagrazia De Palo; Elisa Cattaneo; Caroline Maake; Hubert Rehrauer; Endre Laczko; Michal A Kurowski; Janusz Bujnicki; Mirco Menigatti; Judith Luz; Teresa V Ranalli; Vito Gomes; Alfredo Pastorelli; Roberto Faggiani; Marcello Anti; Josef Jiricny; Hans Clevers; Giancarlo Marra
Transcriptome profile of human colorectal adenomas.
Molecular cancer research : MCR 2007;5(12):1263-75.
2007: Jesse R Zamudio; Bidyottam Mittra; Silvie Foldynová-Trantírková; Gusti Zeiner; Julius Lukes; Janusz Bujnicki; Nancy R Sturm; David A Campbell
The 2'-O-ribose methyltransferase for cap 1 of spliced leader RNA and U1 small nuclear RNA in Trypanosoma brucei.
Molecular and cellular biology 2007;27(17):6084-92.
2007: Jan Kosinski; Elena Kubareva; Janusz Bujnicki
A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering.
Proteins 2007;68(1):324-36.
2007: Arturas Jakubauskas; Jolanta Giedriene; Janusz Bujnicki; Arvydas Janulaitis
Identification of a single HNH active site in type IIS restriction endonuclease Eco31I.
Journal of molecular biology 2007;370(1):157-69.
2007: Michal J Pietal; Irina Tuszynska; Janusz Bujnicki
PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure.
Bioinformatics (Oxford, England) 2007;23(11):1429-30.
2007: Lukasz Koscinski; Marcin Feder; Janusz Bujnicki
Identification of a missing sequence and functionally important residues of 16S rRNA:m(1)A1408 methyltransferase KamB that causes bacterial resistance to aminoglycoside antibiotics.
Cell cycle (Georgetown, Tex.) 2007;6(10):1268-71.
2007: Eva Chovancova; Jan Kosinski; Janusz Bujnicki; Jirí Damborský
Phylogenetic analysis of haloalkane dehalogenases.
Proteins 2007;67(2):305-16.
2007: Jerzy Orlowski; Michal Boniecki; Janusz Bujnicki
I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition.
Bioinformatics (Oxford, England) 2007;23(5):527-30.
2007: Vladimir Pena; Sunbin Liu; Janusz Bujnicki; Reinhard Lührmann; Markus C Wahl
Structure of a multipartite protein-protein interaction domain in splicing factor prp8 and its link to retinitis pigmentosa.
Molecular cell 2007;25(4):615-24.
2007: Sarah G Ozanick; Janusz Bujnicki; Daniel S Sem; James T Anderson
Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding.
Nucleic acids research 2007;35(20):6808-19.
2007: Elena M Ibryashkina; Marina Zakharova; Vladimir B Baskunov; Ekaterina S Bogdanova; Maxim O Nagornykh; Marat M Den'mukhamedov; Bogdan S Melnik; Andrzej Kolinski; Dominik Gront; Marcin Feder; Alexander S Solonin; Janusz Bujnicki
Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily.
BMC structural biology 2007;7():48.
2007: Yang Liu; Zhengjun Li; Qingsong Lin; Jan Kosinski; J Seetharaman; Janusz Bujnicki; J Sivaraman; Choy L Hew
Structure and evolutionary origin of Ca(2+)-dependent herring type II antifreeze protein.
PloS one 2007;2(6):e548.
2007: S Sunita; Elzbieta Purta; Malgorzata Durawa; Karolina L Tkaczuk; J Swaathi; Janusz Bujnicki; J Sivaraman
Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC.
Nucleic acids research 2007;35(13):4264-74.
2007: Joanna M Sasin; Adam Godzik; Janusz Bujnicki
SURF'S UP! - protein classification by surface comparisons.
Journal of biosciences 2007;32(1):97-100.
2007: Karolina L Tkaczuk; Stanislaw Dunin-Horkawicz; Elzbieta Purta; Janusz Bujnicki
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.
BMC bioinformatics 2007;8():73.
2007: Ken-ichi Miyazono; Miki Watanabe; Jan Kosinski; Ken Ishikawa; Masayuki Kamo; Tatsuya Sawasaki; Koji Nagata; Janusz Bujnicki; Yaeta Endo; Masaru Tanokura; Ichizo Kobayashi
Novel protein fold discovered in the PabI family of restriction enzymes.
Nucleic acids research 2007;35(6):1908-18.
2007: Patrick Schäfer; Iwona A Cymerman; Janusz Bujnicki; Gregor Meiss
Human lysosomal DNase IIalpha contains two requisite PLD-signature (HxK) motifs: evidence for a pseudodimeric structure of the active enzyme species.
Protein science : a publication of the Protein Society 2007;16(1):82-91.
2006: Iwona A Cymerman; Agnieszka Obarska; Krzysztof J Skowronek; Arvydas Lubys; Janusz Bujnicki
Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease.
Proteins 2006;65(4):867-76.
2006: Laurent Gros; Axelle Renodon-Cornière; Bruno Robert de Saint Vincent; Marcin Feder; Janusz Bujnicki; Alain Jacquemin-Sablon
Characterization of prmt7alpha and beta isozymes from Chinese hamster cells sensitive and resistant to topoisomerase II inhibitors.
Biochimica et biophysica acta 2006;1760(11):1646-56.
2006: Renata Godlewska; Artur Dzwonek; Michał Mikuła; Jerzy Ostrowski; Marcin Pawłowski; Janusz Bujnicki; Elzbieta K Jagusztyn-Krynicka
Helicobacter pylori protein oxidation influences the colonization process.
International journal of medical microbiology : IJMM 2006;296(4-5):321-4.
2006: Runlin Han; Clayton C Caswell; Ewa Lukomska; Douglas R Keene; Marcin Pawlowski; Janusz Bujnicki; Jiyeun K Kim; Slawomir Lukomski
Binding of the low-density lipoprotein by streptococcal collagen-like protein Scl1 of Streptococcus pyogenes.
Molecular microbiology 2006;61(2):351-67.
2006: Jesse R Zamudio; Bidyottam Mittra; Gusti Zeiner; Marcin Feder; Janusz Bujnicki; Nancy R Sturm; David A Campbell
Complete cap 4 formation is not required for viability in Trypanosoma brucei.
Eukaryotic cell 2006;5(6):905-15.
2006: Krzysztof J Skowronek; Jan Kosinski; Janusz Bujnicki
Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis.
Proteins 2006;63(4):1059-68.
2006: Shivakumara Bheemanaik; Janusz Bujnicki; Valakunja Nagaraja; Desirazu N Rao
Functional analysis of amino acid residues at the dimerisation interface of KpnI DNA methyltransferase.
Biological chemistry 2006;387(5):515-23.
2006: Peter K Chiang; Janusz Bujnicki; Xinzhuan Su; David Lanar
Malaria: therapy, genes and vaccines.
Current molecular medicine 2006;6(3):309-26.
2006: Ewa Sikora; Anna Bielak-Zmijewska; Adriana Magalska; Katarzyna Piwocka; Grazyna Mosieniak; Magdalena Kalinowska; Piotr Widlak; Iwona A Cymerman; Janusz Bujnicki
Curcumin induces caspase-3-dependent apoptotic pathway but inhibits DNA fragmentation factor 40/caspase-activated DNase endonuclease in human Jurkat cells.
Molecular cancer therapeutics 2006;5(4):927-34.
2006: Karolina Klimek-Tomczak; Michal Mikula; Artur Dzwonek; Agnieszka Paziewska; Jakub Karczmarski; Ewa E Hennig; Janusz Bujnicki; Piotr Bragoszewski; Oleg Denisenko; Karol Bomsztyk; Jerzy Ostrowski
Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.
British journal of cancer 2006;94(4):586-92.
2006: Mala Samaranayake; Janusz Bujnicki; Michael Carpenter; Ashok S Bhagwat
Evaluation of molecular models for the affinity maturation of antibodies: roles of cytosine deamination by AID and DNA repair.
Chemical reviews 2006;106(2):700-19.
2006: Michal Mikula; Jakub Karczmarski; Artur Dzwonek; Tymon Rubel; Ewa E Hennig; Michal Dadlez; Janusz Bujnicki; Karol Bomsztyk; Jerzy Ostrowski
Casein kinases phosphorylate multiple residues spanning the entire hnRNP K length.
Biochimica et biophysica acta 2006;1764(2):299-306.
2006: Jutta Metz; Andrea Wächter; Bastian Schmidt; Janusz Bujnicki; Blanche Schwappach
The yeast Arr4p ATPase binds the chloride transporter Gef1p when copper is available in the cytosol.
The Journal of biological chemistry 2006;281(1):410-7.
2006: Agnieszka Wyszyńska; Marcin Pawłowski; Janusz Bujnicki; Dariusz P Pawelec; Jos P M Van Putten; Elzbieta Brzuszkiewicz; Elzbieta K Jagusztyn-Krynicka
Genetic characterisation of the cjaAB operon of Campylobacter coli.
Polish journal of microbiology / Polskie Towarzystwo Mikrobiologów = The Polish Society of Microbiologists 2006;55(2):85-94.
2006: Michael Carpenter; Pradeep Divvela; Vera Pingoud; Janusz Bujnicki; Ashok S Bhagwat
Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI.
Nucleic acids research 2006;34(13):3762-70.
2006: Elzbieta Purta; Françoise van Vliet; Karolina L Tkaczuk; Stanislaw Dunin-Horkawicz; Hirotada Mori; Louis Droogmans; Janusz Bujnicki
The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase.
BMC molecular biology 2006;7():23.
2006: Guillaume Gabant; Sylvie Auxilien; Irina Tuszynska; Marie Locard; Michal J Gajda; Guylaine Chaussinand; Bernard Fernandez; Alain Dedieu; Henri Grosjean; Béatrice Golinelli-Pimpaneau; Janusz Bujnicki; Jean Armengaud
THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain.
Nucleic acids research 2006;34(9):2483-94.
2006: Stanislaw Dunin-Horkawicz; Marcin Feder; Janusz Bujnicki
Phylogenomic analysis of the GIY-YIG nuclease superfamily.
BMC genomics 2006;7():98.
2006: Agnieszka Obarska; Alex Blundell; Marcin Feder; Stepánka Vejsadová; Eva Sisáková; Marie Weiserová; Janusz Bujnicki; Keith Firman
Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA.
Nucleic acids research 2006;34(7):1992-2005.
2006: Ingrid Zegers; Daniel Gigot; Françoise van Vliet; Catherine Tricot; Stéphane Aymerich; Janusz Bujnicki; Jan Kosinski; Louis Droogmans
Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase.
Nucleic acids research 2006;34(6):1925-34.
2006: Karolina L Tkaczuk; Agnieszka Obarska; Janusz Bujnicki
Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis.
BMC evolutionary biology 2006;6():6.
2006: Stanislaw Dunin-Horkawicz; Anna Czerwoniec; Michal J Gajda; Marcin Feder; Henri Grosjean; Janusz Bujnicki
MODOMICS: a database of RNA modification pathways.
Nucleic acids research 2006;34(Database issue):D145-9.
2006: Janusz Bujnicki
Protein-structure prediction by recombination of fragments.
Chembiochem : a European journal of chemical biology 2006;7(1):19-27.
2005: Elena Armalyte; Janusz Bujnicki; Jolanta Giedriene; Giedrius Gasiunas; Jan Kosiński; Arvydas Lubys
Mva1269I: a monomeric type IIS restriction endonuclease from Micrococcus varians with two EcoRI- and FokI-like catalytic domains.
The Journal of biological chemistry 2005;280(50):41584-94.
2005: Iwona A Cymerman; Gregor Meiss; Janusz Bujnicki
DNase II is a member of the phospholipase D superfamily.
Bioinformatics (Oxford, England) 2005;21(21):3959-62.
2005: Jan Kosinski; Ina Steindorf; Janusz Bujnicki; Luis Giron-Monzon; Peter Friedhoff
Analysis of the quaternary structure of the MutL C-terminal domain.
Journal of molecular biology 2005;351(4):895-909.
2005: Vera Pingoud; Hildegard Geyer; Rudolf Geyer; Elena Kubareva; Janusz Bujnicki; Alfred Pingoud
Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII.
Molecular bioSystems 2005;1(2):135-41.
2005: Suresh K Purushothaman; Janusz Bujnicki; Henri Grosjean; Bruno Lapeyre
Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA.
Molecular and cellular biology 2005;25(11):4359-70.
2005: Elzbieta Purta; Françoise van Vliet; Catherine Tricot; Lara G De Bie; Marcin Feder; Krzysztof J Skowronek; Louis Droogmans; Janusz Bujnicki
Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis.
Proteins 2005;59(3):482-8.
2005: Agnieszka A Chmiel; Monika Radlinska; Sebastian D Pawlak; Daniel Krowarsch; Janusz Bujnicki; Krzysztof J Skowronek
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.
Protein engineering, design & selection : PEDS 2005;18(4):181-9.
2005: Vera Pingoud; Anna Sudina; Hildegard Geyer; Janusz Bujnicki; Rudi Lurz; Gerhild Lüder; Richard Morgan; Elena Kubareva; Alfred Pingoud
Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences.
The Journal of biological chemistry 2005;280(6):4289-98.
2005: Monika Radlinska; Aneta Kondrzycka-Dada; Andrzej Piekarowicz; Janusz Bujnicki
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.
Proteins 2005;58(2):263-70.
2005: Monika Radlińska; Andrzej Piekarowicz; Marc Galimand; Janusz Bujnicki
Cloning and preliminary characterization of a GATC-specific beta2-class DNA:m6A methyltransferase encoded by transposon Tn1549 from Enterococcus spp.
Polish journal of microbiology / Polskie Towarzystwo Mikrobiologów = The Polish Society of Microbiologists 2005;54(3):249-52.
2005: Jan Kosinski; Michal J Gajda; Iwona A Cymerman; Michal A Kurowski; Marcin Pawlowski; Michal Boniecki; Agnieszka Obarska; Grzegorz Papaj; Paulina Sroczynska-Obuchowicz; Karolina L Tkaczuk; Paulina Sniezynska; Joanna M Sasin; Anna Augustyn; Janusz Bujnicki; Marcin Feder
FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6.
Proteins 2005;61 Suppl 7():106-13.
2005: Andrzej Koliński; Janusz Bujnicki
Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.
Proteins 2005;61 Suppl 7():84-90.
2005: Ken Ishikawa; Miki Watanabe; Toshihiro Kuroita; Ikuo Uchiyama; Janusz Bujnicki; Bunsei Kawakami; Masaru Tanokura; Ichizo Kobayashi
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.
Nucleic acids research 2005;33(13):e112.
2005: Jan Kosinski; Marcin Feder; Janusz Bujnicki
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.
BMC bioinformatics 2005;6():172.
2005: Marcin Feder; Janusz Bujnicki
Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site.
BMC genomics 2005;6():21.
2005: Sebastian D Pawlak; Monika Radlinska; Agnieszka A Chmiel; Janusz Bujnicki; Krzysztof J Skowronek
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.
Nucleic acids research 2005;33(2):661-71.
2005: Agnieszka A Chmiel; Janusz Bujnicki; Krzysztof J Skowronek
A homology model of restriction endonuclease SfiI in complex with DNA.
BMC structural biology 2005;5():2.
2005: Anna Raczko; Janusz Bujnicki; Marcin Pawlowski; Renata Godlewska; Malgorzata Lewandowska; Elzbieta K Jagusztyn-Krynicka
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.
Microbiology (Reading, England) 2005;151(Pt 1):219-31.
2004: Xiaoduan Ye; Patrick K O'Neil; Adrienne N Foster; Michal J Gajda; Jan Kosinski; Michal A Kurowski; Janusz Bujnicki; Alan Friedman; Chris Bailey-Kellogg
Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure.
Protein science : a publication of the Protein Society 2004;13(12):3298-313.
2004: Elizaveta V Koudan; Janusz Bujnicki; Elizaveta S Gromova
Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy.
Journal of biomolecular structure & dynamics 2004;22(3):339-45.
2004: Agnieszka Paziewska; Lucjan S Wyrwicz; Janusz Bujnicki; Karol Bomsztyk; Jerzy Ostrowski
Cooperative binding of the hnRNP K three KH domains to mRNA targets.
FEBS letters 2004;577(1-2):134-40.
2004: Jean Armengaud; Jaunius Urbonavicius; Bernard Fernandez; Guylaine Chaussinand; Janusz Bujnicki; Henri Grosjean
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.
The Journal of biological chemistry 2004;279(35):37142-52.
2004: Janusz Bujnicki; Yamina Oudjama; Martine Roovers; Sylwia Owczarek; Joël Caillet; Louis Droogmans
Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA.
RNA (New York, N.Y.) 2004;10(8):1236-42.
2004: Joanna M Sasin; Janusz Bujnicki
COLORADO3D, a web server for the visual analysis of protein structures.
Nucleic acids research 2004;32(Web Server issue):W586-9.
2004: Patrick Schäfer; Sebastian R Scholz; Oleg Gimadutdinow; Iwona A Cymerman; Janusz Bujnicki; Adolf Ruiz-Carrillo; Alfred Pingoud; Gregor Meiss
Structural and functional characterization of mitochondrial EndoG, a sugar non-specific nuclease which plays an important role during apoptosis.
Journal of molecular biology 2004;338(2):217-28.
2004: W David Nes; Pruthvi Jayasimha; Wenxu Zhou; Ragu Kanagasabai; Changxiao Jin; Tahhan T Jaradat; Robert W Shaw; Janusz Bujnicki
Sterol methyltransferase: functional analysis of highly conserved residues by site-directed mutagenesis.
Biochemistry 2004;43(2):569-76.
2004: Matheshwaran Saravanan; Janusz Bujnicki; Iwona A Cymerman; Desirazu N Rao; Valakunja Nagaraja
Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily.
Nucleic acids research 2004;32(20):6129-35.
2004: Janusz Bujnicki; Marcin Feder; Chastity L Ayres; Kent L Redman
Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases.
Nucleic acids research 2004;32(8):2453-63.
2004: G Maravić; Janusz Bujnicki; Mirna Flögel
Mutational analysis of basic residues in the N-terminus of the rRNA:m6A methyltransferase ErmC'.
Folia microbiologica 2004;49(1):3-7.
2004: Shobha Potluri; A A Khan; A Kuzminykh; Janusz Bujnicki; Alan Friedman; Chris Bailey-Kellogg
Geometric analysis of cross-linkability for protein fold discrimination.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2004;():447-58.
2004: Martine Roovers; Johan Wouters; Janusz Bujnicki; Catherine Tricot; Victor Stalon; Henri Grosjean; Louis Droogmans
A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase.
Nucleic acids research 2004;32(2):465-76.
2003: Michal A Kurowski; Ashok S Bhagwat; Grzegorz Papaj; Janusz Bujnicki
Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB.
BMC genomics 2003;4(1):48.
2003: Janusz Bujnicki
Crystallographic and bioinformatic studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology.
Current protein & peptide science 2003;4(5):327-37.
2003: Gordana Maravić; Marcin Feder; Sandor Pongor; Mirna Flögel; Janusz Bujnicki
Mutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC'.
Journal of molecular biology 2003;332(1):99-109.
2003: Richard Gordon; Krzysztof Ginalski; Witold R Rudnicki; Leszek Rychlewski; Marvin C Pankaskie; Janusz Bujnicki; Peter K Chiang
Anti-HIV-1 activity of 3-deaza-adenosine analogs. Inhibition of S-adenosylhomocysteine hydrolase and nucleotide congeners.
European journal of biochemistry / FEBS 2003;270(17):3507-17.
2003: Janusz Bujnicki; Sean T Prigge; Diana Caridha; Peter K Chiang
Structure, evolution, and inhibitor interaction of S-adenosyl-L-homocysteine hydrolase from Plasmodium falciparum.
Proteins 2003;52(4):624-32.
2003: Gordana Maravić; Janusz Bujnicki; Marcin Feder; Sandor Pongor; Mirna Flögel
Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions.
Nucleic acids research 2003;31(16):4941-9.
2003: John Mouaikel; Janusz Bujnicki; Jamal Tazi; Rémy Bordonné
Sequence-structure-function relationships of Tgs1, the yeast snRNA/snoRNA cap hypermethylase.
Nucleic acids research 2003;31(16):4899-909.
2003: Janusz Bujnicki; Megan A Albert; Donald J Nelson; David L Thurlow
Fold recognition, homology modeling, docking simulations, kinetics analysis and mutagenesis of ATP/CTP:tRNA nucleotidyltransferase from Methanococcus jannaschii.
Proteins 2003;52(3):349-59.
2003: Sebastian R Scholz; Christian Korn; Janusz Bujnicki; Oleg Gimadutdinow; Alfred Pingoud; Gregor Meiss
Experimental evidence for a beta beta alpha-Me-finger nuclease motif to represent the active site of the caspase-activated DNase.
Biochemistry 2003;42(31):9288-94.
2003: Krzysztof Ginalski; Jakub Paś; Lucjan S Wyrwicz; Marcin von Grotthuss; Janusz Bujnicki; Leszek Rychlewski
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure.
Nucleic acids research 2003;31(13):3804-7.
2003: Michal A Kurowski; Janusz Bujnicki
GeneSilico protein structure prediction meta-server.
Nucleic acids research 2003;31(13):3305-7.
2003: Vera Pingoud; Charlotte Conzelmann; Steffen Kinzebach; Anna Sudina; Valeri Metelev; Elena Kubareva; Janusz Bujnicki; Rudi Lurz; Gerhild Lüder; Shuang-Yong Xu; Alfred Pingoud
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.
Journal of molecular biology 2003;329(5):913-29.
2003: Lara G S De Bie; Martine Roovers; Yamina Oudjama; Ruddy Wattiez; Catherine Tricot; Victor Stalon; Louis Droogmans; Janusz Bujnicki
The yggH gene of Escherichia coli encodes a tRNA (m7G46) methyltransferase.
Journal of bacteriology 2003;185(10):3238-43.
2003: Louis Droogmans; Martine Roovers; Janusz Bujnicki; Catherine Tricot; Thomas Hartsch; Victor Stalon; Henri Grosjean
Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures.
Nucleic acids research 2003;31(8):2148-56.
2003: Michal A Kurowski; Joanna M Sasin; Marcin Feder; Janusz Debski; Janusz Bujnicki
Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures.
BMC bioinformatics 2003;4():9.
2003: Vladimir Tchernaenko; Monika Radlinska; Christopher Drabik; Janusz Bujnicki; Herbert R Halvorson; Leonard C Lutter
Topological measurement of an A-tract bend angle: comparison of the bent and straightened states.
Journal of molecular biology 2003;326(3):737-49.
2003: Marcin Feder; Jakub Paś; Lucjan S Wyrwicz; Janusz Bujnicki
Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases.
Gene 2003;302(1-2):129-38.
2003: Jan Kosinski; Iwona A Cymerman; Marcin Feder; Michal A Kurowski; Joanna M Sasin; Janusz Bujnicki
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.
Proteins 2003;53 Suppl 6():369-79.
2003: Joanna M Sasin; Michal A Kurowski; Janusz Bujnicki
STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification.
Bioinformatics (Oxford, England) 2003;19 Suppl 1():i252-4.
2002: Janusz Bujnicki; Leszek Rychlewski; Daniel Fischer
Fold-recognition detects an error in the Protein Data Bank.
Bioinformatics (Oxford, England) 2002;18(10):1391-5.
2002: Janusz Bujnicki; Marcin Feder; Monika Radlinska; Robert Blumenthal
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.
Journal of molecular evolution 2002;55(4):431-44.
2002: Janusz Bujnicki; Marcin Feder; Leszek Rychlewski; Daniel Fischer
Errors in the D. radiodurans large ribosomal subunit structure detected by protein fold-recognition and structure validation tools.
FEBS letters 2002;525(1-3):174-5.
2002: Renata Godlewska; Janusz Bujnicki; Jerzy Ostrowski; Elzbieta K Jagusztyn-Krynicka
The hppA gene of Helicobacter pylori encodes the class C acid phosphatase precursor.
FEBS letters 2002;525(1-3):39-42.
2002: Yi Xu; Douglas R Keene; Janusz Bujnicki; Magnus Höök; Slawomir Lukomski
Streptococcal Scl1 and Scl2 proteins form collagen-like triple helices.
The Journal of biological chemistry 2002;277(30):27312-8.
2002: Janusz Bujnicki; Richard A Leach; Janusz Debski; Leszek Rychlewski
Bioinformatic analyses of the tRNA: (guanine 26, N2,N2)-dimethyltransferase (Trm1) family.
Journal of molecular microbiology and biotechnology 2002;4(4):405-15.
2002: Janusz Bujnicki; Leszek Rychlewski
Fold-recognition analysis predicts that the Tag protein family shares a common domain with the helix-hairpin-helix DNA glycosylases.
DNA repair 2002;1(5):391-5.
2002: Vera Pingoud; Elena Kubareva; Gudrun Stengel; Peter Friedhoff; Janusz Bujnicki; Claus Urbanke; Anna Sudina; Alfred Pingoud
Evolutionary relationship between different subgroups of restriction endonucleases.
The Journal of biological chemistry 2002;277(16):14306-14.
2002: Janusz Bujnicki; Leszek Rychlewski
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.
BMC bioinformatics 2002;3():10.
2002: Lionel Pintard; François Lecointe; Janusz Bujnicki; Claire Bonnerot; Henri Grosjean; Bruno Lapeyre
Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop.
The EMBO journal 2002;21(7):1811-20.
2002: Janusz Bujnicki
Sequence permutations in the molecular evolution of DNA methyltransferases.
BMC evolutionary biology 2002;2():3.
2002: Lionel Pintard; Janusz Bujnicki; Bruno Lapeyre; Claire Bonnerot
MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase.
The EMBO journal 2002;21(5):1139-47.
2002: Janusz Bujnicki; Leszek Rychlewski
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.
Protein engineering 2002;15(2):101-8.
2002: Pent Zhang; Diarmuid E Nicholson; Janusz Bujnicki; Xinzhuan Su; James J Brendle; Michael Ferdig; Dennis E Kyle; Wilbur K Milhous; Peter K Chiang
Angiogenesis inhibitors specific for methionine aminopeptidase 2 as drugs for malaria and leishmaniasis.
Journal of biomedical science 2002;9(1):34-40.
2002: Janusz Bujnicki; Robert Blumenthal; Leszek Rychlewski
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.
Journal of molecular microbiology and biotechnology 2002;4(1):93-9.
2001: J Lundström; L Rychlewski; Janusz Bujnicki; Arne Elofsson
Pcons: a neural-network-based consensus predictor that improves fold recognition.
Protein science : a publication of the Protein Society 2001;10(11):2354-62.
2001: Janusz Bujnicki
In silico analysis of the tRNA:m1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea.
FEBS letters 2001;507(2):123-7.
2001: Janusz Bujnicki; Piotr Rotkiewicz; Andrzej Kolinski; Leszek Rychlewski
Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics.
Protein engineering 2001;14(10):717-21.
2001: Janusz Bujnicki; A Elofsson; D Fischer; Leszek Rychlewski
Structure prediction meta server.
Bioinformatics (Oxford, England) 2001;17(8):750-1.
2001: Janusz Bujnicki; Leszek Rychlewski
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.
Gene 2001;267(2):183-91.
2001: Janusz Bujnicki; Leszek Rychlewski
Unusual evolutionary history of the tRNA splicing endonuclease EndA: relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases.
Protein science : a publication of the Protein Society 2001;10(3):656-60.
2001: Janusz Bujnicki; Leszek Rychlewski
The herpesvirus alkaline exonuclease belongs to the restriction endonuclease PD-(D/E)XK superfamily: insight from molecular modeling and phylogenetic analysis.
Virus genes 2001;22(2):219-30.
2001: Janusz Bujnicki; A Elofsson; D Fischer; Leszek Rychlewski
LiveBench-1: continuous benchmarking of protein structure prediction servers.
Protein science : a publication of the Protein Society 2001;10(2):352-61.
2001: Janusz Bujnicki; Monika Radlinska; Piotr Zaleski; Andrzej Piekarowicz
Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage.
Acta biochimica Polonica 2001;48(4):969-83.
2001: Janusz Bujnicki
Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons.
Acta biochimica Polonica 2001;48(4):935-67.
2001: Janusz Bujnicki
A model of structure and action of Sau3AI restriction endonuclease that comprises two MutH-like endonuclease domains within a single polypeptide.
Acta microbiologica Polonica 2001;50(3-4):219-31.
2001: Janusz Bujnicki; A Elofsson; D Fischer; L Rychlewski
LiveBench-2: large-scale automated evaluation of protein structure prediction servers.
Proteins 2001;Suppl 5():184-91.
2001: Monika Radlinska; Janusz Bujnicki
Site-directed mutagenesis defines the catalytic aspartate in the active site of the atypical DNA: m4C methyltransferase M.NgoMXV.
Acta microbiologica Polonica 2001;50(2):97-105.
2001: Monika Radlinska; Janusz Bujnicki
Cloning of enterohemorrhagic Escherichia coli phage VT-2 dam methyltransferase.
Acta microbiologica Polonica 2001;50(2):161-7.
2001: Janusz Bujnicki; Monika Radlinska
Cloning and characterization of M.LmoA118I, a novel DNA:m4C methyltransferase from the Listeria monocytogenes phage A118, a close homolog of M.NgoMXV.
Acta microbiologica Polonica 2001;50(2):155-60.
2001: Janusz Bujnicki; Leszek Rychlewski
Reassignment of specificities of two cap methyltransferase domains in the reovirus lambda 2 protein.
Genome biology 2001;2(9):RESEARCH0038.
2001: Janusz Bujnicki; Leszek Rychlewski
Sequence analysis and structure prediction of aminoglycoside-resistance 16S rRNA:m7G methyltransferases.
Acta microbiologica Polonica 2001;50(1):7-17.
2001: Janusz Bujnicki; Marcin Feder; Monika Radlinska; Leszek Rychlewski
mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships.
BMC bioinformatics 2001;2():2.
2001: Janusz Bujnicki; Leszek Rychlewski
Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles.
Journal of molecular microbiology and biotechnology 2001;3(1):69-72.
2001: Janusz Bujnicki; Monika Radlinska; Leszek Rychlewski
Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed.
Trends in biochemical sciences 2001;26(1):9-11.
2000: Janusz Bujnicki; L Rychlewski
Prediction of a common fold for all four subunits of the yeast tRNA splicing endonuclease: implications for the evolution of the EndA/Sen family.
FEBS letters 2000;486(3):328-9.
2000: Janusz Bujnicki
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.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2000;14(14):2365-8.
2000: Janusz Bujnicki; M Radlinska; L Rychlewski
Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc finger and structural similarity to betabetaalphaMe endonucleases.
Molecular microbiology 2000;37(5):1280-1.
2000: Janusz Bujnicki
Homology modelling of the DNA 5mC methyltransferase M.BssHII. Is permutation of functional subdomains common to all subfamilies of DNA methyltransferases?
International journal of biological macromolecules 2000;27(3):195-204.
2000: Janusz Bujnicki; Leszek Rychlewski
Prediction of a novel RNA 2'-O-ribose methyltransferase subfamily encoded by the Escherichia coli YgdE open reading frame and its orthologs.
Acta microbiologica Polonica 2000;49(3-4):253-60.
2000: Janusz Bujnicki
Sequence, structural, and evolutionary analysis of prokaryotic ribosomal protein L11 methyltransferases.
Acta microbiologica Polonica 2000;49(1):19-29.
2000: Janusz Bujnicki
Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures.
Journal of molecular evolution 2000;50(1):39-44.
1999: Monika Radlinska; Janusz Bujnicki; Andrzej Piekarowicz
Structural characterization of two tandemly arranged DNA methyltransferase genes from Neisseria gonorrhoeae MS11: N4-cytosine specific M.NgoMXV and nonfunctional 5-cytosine-type M.NgoMorf2P.
Proteins 1999;37(4):717-28.
1999: Janusz Bujnicki; Monika Radlinska
Molecular evolution of DNA-(cytosine-N4) methyltransferases: evidence for their polyphyletic origin.
Nucleic acids research 1999;27(22):4501-9.
1999: Janusz Bujnicki; Monika Radlinska
Is the HemK family of putative S-adenosylmethionine-dependent methyltransferases a "missing" zeta subfamily of adenine methyltransferases? A hypothesis.
IUBMB life 1999;48(3):247-9.
1999: Janusz Bujnicki
Comparison of protein structures reveals monophyletic origin of the AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation.
In silico biology 1999;1(4):175-82.
1999: Andrzej Piekarowicz; Janusz Bujnicki
Cloning of the Dam methyltransferase gene from Haemophilus influenzae bacteriophage HP1.
Acta microbiologica Polonica 1999;48(2):123-9.
1999: Janusz Bujnicki; Monika Radlinska
Molecular phylogenetics of DNA 5mC-methyltransferases.
Acta microbiologica Polonica 1999;48(1):19-30.