All publications
2025
Determining the effects of pseudouridine incorporation on human tRNAs.
Biela AD, Nowak JS, Biela AP, Mukherjee S, Moafinejad SN, Maiti S, Chramiec-Głąbik A, Mehta R, Jeżowski J, Dobosz D, Dahate P, Arluison V, Wien F, Indyka P, Rawski M, Bujnicki JM, Lin TY, Glatt S.
EMBO J. 2025
Protein-RNA Docking Benchmark v3.0 Integrated With Binding Affinity.
Kant S, Nithin C, Mukherjee S, Maity A, Bahadur RP.
Proteins. 2025
DesiRNA: structure-based design of RNA sequences with a replica exchange Monte Carlo approach.
Wirecki TK, Lach G, Badepally NG, Moafinejad SN, Jaryani F, Klaudel G, Nec K, Baulin EF, Bujnicki JM.
Nucleic Acids Res. 2025
RNA-Puzzles Round V: blind predictions of 23 RNA structures.
Bu F, Adam Y, Adamiak RW, Antczak M, de Aquino BRH, Badepally NG, Batey RT, Baulin EF, Boinski P, Boniecki MJ, Bujnicki JM, Carpenter KA, Chacon J, Chen SJ, Chiu W, Cordero P, Das NK, Das R, Dawson WK, DiMaio F, Ding F, Dock-Bregeon AC, Dokholyan NV, Dror RO, Dunin-Horkawicz S, Eismann S, Ennifar E, Esmaeeli R, Farsani MA, Ferré-D'Amaré AR, Geniesse C, Ghanim GE, Guzman HV, Hood IV, Huang L, Jain DS, Jaryani F, Jin L, Joshi A, Karelina M, Kieft JS, Kladwang W, Kmiecik S, Koirala D, Kollmann M, Kretsch RC, Kurciński M, Li J, Li S, Magnus M, Masquida B, Moafinejad SN, Mondal A, Mukherjee S, Nguyen THD, Nikolaev G, Nithin C, Nye G, Pandaranadar Jeyeram IPN, Perez A, Pham P, Piccirilli JA, Pilla SP, Pluta R, Poblete S, Ponce-Salvatierra A, Popenda M, Popenda L, Pucci F, Rangan R, Ray A, Ren A, Sarzynska J, Sha CM, Stefaniak F, Su Z, Suddala KC, Szachniuk M, Townshend R, Trachman RJ 3rd, Wang J, Wang W, Watkins A, Wirecki TK, Xiao Y, Xiong P, Xiong Y, Yang J, Yesselman JD, Zhang J, Zhang Y, Zhang Z, Zhou Y, Zok T, Zhang D, Zhang S, Żyła A, Westhof E, Miao Z.
Nat Methods. 2025
Sci-ModoM: a quantitative database of transcriptome-wide high-throughput RNA modification sites.
Boileau E, Wilhelmi H, Busch A, Cappannini A, Hildebrand A, Bujnicki JM, Dieterich C.
Nucleic Acids Res . 2025
NAIRDB: a database of Fourier transform infrared (FTIR) data for nucleic acids.
Balduzzi E, Geinguenaud F, Sordyl D, Maiti S, Farsani MA, Nikolaev G, Arluison V, Bujnicki JM.
Nucleic Acids Res. 2025
2024
Role of Non-Canonical Stacking Interactions of Heterocyclic RNA Bases in Ribosome Function.
Metelev VG, Baulin EF, Bogdanov AA.
Biochemistry (Mosc). 2024
Cryo-EM structure of raiA ncRNA from Clostridium reveals a new RNA 3D fold.
Goud Badepally N, Rocha de Moura T, Purta E, Baulin EF, Bujnicki JM.
J Mol Biol. 2024
The three YTHDF paralogs and VIRMA are strong cross-histotype tumor driver candidates among m6A core genes.
Destefanis E, Sighel D, Dalfovo D, Gilmozzi R, Broso F, Cappannini A, Bujnicki JM, Romanel A, Dassi E, Quattrone A.
NAR Cancer. 2024
Advances in the field of RNA 3D structure prediction and modeling, with purely theoretical approaches, and with the use of experimental data.
Mukherjee S, Moafinejad SN, Badepally NG, Merdas K, Bujnicki JM.
Structure. 2024
Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens.
Perlinska AP, Nguyen ML, Pilla SP, Staszor E, Lewandowska I, Bernat A, Purta E, Augustyniak R, Bujnicki JM, Sulkowska JI.
Front Mol Biosci. 2024
SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories.
Moafinejad SN, de Aquino BRH, Boniecki MJ, Jeyeram IPNP, Nikolaev G, Magnus M, Farsani MA, Badepally NG, Wirecki TK, Stefaniak F, Bujnicki JM.
Nucleic Acids Res. 2024
ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment.
Bohdan DR, Bujnicki JM, Baulin EF.
Nucleic Acids Res. 2024
Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes.
de Moura TR, Purta E, Bernat A, Martín-Cuevas EM, Kurkowska M, Baulin EF, Mukherjee S, Nowak J, Biela AP, Rawski M, Glatt S, Moreno-Herrero F, Bujnicki JM.
Nucleic Acids Res.. 2024
Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology.
Niemyska W, Mukherjee S, Gren BA, Niewieczerzal S, Bujnicki JM, Sulkowska JI.
J Mol Biol.. 2024
MODOMICS: a database of RNA modifications and related information. 2023 update.
Cappannini A, Ray A, Purta E, Mukherjee S, Boccaletto P, Moafinejad SN, Lechner A, Barchet C, Klaholz BP, Stefaniak F, Bujnicki JM.
Nucleic Acids Res. . 2024
DEGRONOPEDIA: a web server for proteome-wide inspection of degrons.
Szulc NA, Stefaniak F, Piechota M, Soszyńska A, Piórkowska G, Cappannini A, Bujnicki JM, Maniaci C, Pokrzywa W.
Nucleic Acids Res. 2024
2023
DesiRNA: structure-based design of RNA sequences with a Monte Carlo approach.
Wirecki T, Lach G, Jaryani F, Badepally NG, Moafinejad SN, Klaudel G, Bujnicki JM.
bioRxiv. 2023
SQUARNA - an RNA secondary structure prediction method based on a greedy stem formation model.
Bohdan DR, Nikolaev GI, Bujnicki JM, Baulin EF
bioRxiv. 2023
RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints.
Baulin EF, Mukherjee S, Moafinejad SN, Wirecki TK, Badepally NG, Jaryani F, Stefaniak F, Amiri Farsani M, Ray A, Rocha de Moura T, Bujnicki JM.
Proteins. 2023
RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints.
Chojnowski G, Zaborowski R, Magnus M, Mukherjee S, Bujnicki JM.
Bioinformatics. 2023
RNA target highlights in CASP15: Evaluation of predicted models by structure providers.
Kretsch RC, Andersen ES, Bujnicki JM, Chiu W, Das R, Luo B, Masquida B, McRae EKS, Schroeder GM, Su Z, Wedekind JE, Xu L, Zhang K, Zheludev IN, Moult J, Kryshtafovych A.
Proteins. 2023
Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing.
Luo BN et al. with Bujnicki JM.
Nature Catalysis. 2023
A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.
Bohdan DR, Voronina VV, Bujnicki JM, Baulin EF.
Nucleic Acids Res.. 2023
Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to RNA.
Szulc NA, Mackiewicz Z, Bujnicki JM, Stefaniak F.
Brief Bioinform.. 2023
Structural basis of sRNA RsmZ regulation of Pseudomonas aeruginosa virulence.
Jia X, Pan Z, Yuan Y, Luo B, Luo Y, Mukherjee S, Jia G, Liu L, Ling X, Yang X, Miao Z, Wei X, Bujnicki JM, Zhao K, Su Z.
Cell Res.. 2023
NACDDB: Nucleic Acid Circular Dichroism Database.
Cappannini A, Mosca K, Mukherjee S, Moafinejad SN, Sinden RR, Arluison V, Bujnicki J, Wien F.
Nucleic Acids Res.. 2023
1D2DSimScore: A novel method for comparing contacts in biomacromolecules and their complexes.
Moafinejad SN,
Protein Sci.. 2023
2022
Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field.
Sieradzan AK, Czaplewski C, Krupa P, Mozolewska MA, Karczyńska AS, Lipska AG, Lubecka EA, Gołaś E, Wirecki T, Makowski M, Ołdziej S, Liwo A.
Methods Mol Biol. 2022
Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models.
Gumna J, Antczak M, Adamiak RW, Bujnicki JM, Chen SJ, Ding F, Ghosh P, Li J, Mukherjee S, Nithin C, Pachulska-Wieczorek K, Ponce-Salvatierra A, Popenda M, Sarzynska J, Wirecki T, Zhang D, Zhang S, Zok T, Westhof E, Miao Z, Szachniuk M, Rybarczyk A.
Int J Mol Sci. 2022
fingeRNAt-A novel tool for high-throughput analysis of nucleic acid-ligand interactions.
Szulc NA, Mackiewicz Z, Bujnicki JM, Stefaniak F.
PLoS Comput Biol.. 2022
Molecular insights into RNA recognition and gene regulation by the TRIM-NHL protein Mei-P26.
Salerno-Kochan A, Horn A, Ghosh P, Nithin C, Kościelniak A, Meindl A, Strauss D, Krutyhołowa R, Rossbach O, Bujnicki JM, Gaik M, Medenbach J, Glatt S.
Life Sci Alliance. 2022
DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes.
Mohammadi-Arani R, Javadi-Zarnaghi F, Boccaletto P, Bujnicki JM, Ponce-Salvatierra A.
Nucleic Acids Res. 2022
2021
Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA.
Nucleic Acids Res.. 2021
AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses.
Stefaniak F, Bujnicki JM.
PLoS Comput Biol.. 2021
RNA and DNA G-quadruplexes bind to human dicer and inhibit its activity.
Koralewska N, Szczepanska A, Ciechanowska K, Wojnicka M, Pokornowska M, Milewski MC, Gudanis D, Baranowski D, Nithin C, Bujnicki JM, Gdaniec Z, Figlerowicz M, Kurzynska-Kokorniak A.
Cell Mol Life Sci.. 2021
DNAmoreDB, a database of DNAzymes.
Ponce-Salvatierra A, Boccaletto P, Bujnicki JM.
Nucleic Acids Res.. 2021
2020
Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements.
Manfredonia I, Nithin C, Ponce-Salvatierra A, Ghosh P, Wirecki TK, Marinus T, Ogando NS, Snijder EJ, van Hemert MJ, Bujnicki JM, Incarnato D.
Nucleic Acids Res. 2020
Luciferase reporter assay for small-molecule inhibitors of MIR92b-3p function: Screening cyanopeptolins produced by Nostoc from the Baltic Sea.
Brzuzan P, Mazur-Marzec H, Florczyk M, Stefaniak F, Fidor A, Konkel R, Woźny M.
Toxicol In Vitro.. 2020
Benzoxazepine-Derived Selective, Orally Bioavailable Inhibitor of Human Acidic Mammalian Chitinase.
Andryianau G, Kowalski M, Piotrowicz MC, Rajkiewicz AA, Dymek B, Sklepkiewicz PL, Pluta E, Stefaniak F, Czestkowski W, Olejniczak S, Mazur M, Niedziejko P, Koralewski R, Matyszewski K, Gruza M, Zagozdzon A, Salamon M, Rymaszewska A, Welzer M, Dzwonek K, Golab J, Olczak J, Bartoszewicz A, Golebiowski A.
ACS Med Chem Lett.. 2020
RNAProbe: a web server for normalization and analysis of RNA structure probing data.
Wirecki TK, Merdas K, Bernat A, Boniecki MJ, Bujnicki JM, Stefaniak F.
Nucleic Acids Res. . 2020
RNA-Puzzles Round IV: 3D Structure Predictions of Four Ribozymes and Two Aptamers.
Miao Z et al. (Boniecki MJ, Bujnicki JM, Joshi A, Magnus M, Piatkowski P, Pluta R.)
RNA. 2020
Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition.
Lambert AR, Hallinan JP, Werther R, Głów D, Stoddard BL.
Structure. 2020
RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.
Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM, Westhof E, Szachniuk M, Miao Z.
Nucleic Acids Res.. 2020
A combined structural and biochemical approach reveals translocation and stalling of UvrB on the DNA lesion as a mechanism of damage verification in bacterial nucleotide excision repair.
Jaciuk M, Swuec P, Gaur V, Kasprzak JM, Renault L, Dobrychłop M, Nirwal S, Bujnicki JM, Costa A, Nowotny M.
DNA Repair (Amst).. 2020
2019
Development of Dual Chitinase Inhibitors as Potential New Treatment for Respiratory System Diseases.
Mazur M, Dymek B, Koralewski R, Sklepkiewicz P, Olejniczak S, Mazurkiewicz M, Piotrowicz M, Salamon M, Jędrzejczak K, Zagozdzon A, Czestkowski W, Matyszewski K, Borek B, Bartoszewicz A, Pluta E, Rymaszewska A, Mozga W, Stefaniak F, Dobrzański P, Dzwonek K, Golab J, Golebiowski A, Olczak J.
J Med Chem. . 2019
Improving selectivity of DNA-RNA binding zinc finger using directed evolution.
Sulej AA
BMC Res Notes. . 2019
RRMdb – an evolutionary-oriented database of RNA recognition motif sequences.
Nowacka M, Boccaletto P, Jankowska E, Jarzynka T, Bujnicki JM, Dunin-Horkawicz S.
Database. 2019
Matching tRNA modifications in humans to their known and predicted enzymes.
de Crecy-Lagard V, Boccaletto P, Mangleburg C, Sharma P, Lowe T, Leidel S, Bujnicki JM.
Nucleic Acids Res.. 2019
QRNAS: software tool for refinement of nucleic acid structures.
Stasiewicz J, Mukherjee S, Nithin C, Bujnicki JM.
BMC Struct Biol. . 2019
RNAcentral: a hub of information for non-coding RNA sequences.
The RNAcentral Consortium (Bujnicki JM, Boccaletto P)
Nucleic Acids Res. . 2019
Petri net-based model of the human DNA base excision repair pathway.
Radom M, Machnicka MA, Krwawicz J, Bujnicki JM, Formanowicz P
PLoS One. 2019
RNA 3D structure prediction guided by independent folding of homologous sequences.
Magnus M, Kappel K, Das R, Bujnicki JM
BMC Bioinformatics. 2019
Specific interaction of zinc finger protein Com with RNA and the crystal structure of a self-complementary RNA duplex recognized by Com.
Nowacka M, Fernandes H, Kiliszek A, Bernat A, Lach G, Bujnicki JM.
PLoS One. 2019
Crystal Structure and Directed Evolution of Specificity of NlaIV Restriction Endonuclease.
Czapinska H, Siwek W, Szczepanowski RH, Bujnicki JM, Bochtler M, Skowronek KJ.
J Mol Biol.. 2019
Structural bases of peptidoglycan recognition by lysostaphin SH3b domain.
Mitkowski P, Jagielska E, Nowak E, Bujnicki JM, Stefaniak F, Niedziałek D, Bochtler M, Sabała I.
Sci Rep.. 2019
Computational modeling of RNA 3D structure based on experimental data.
Ponce-Salvatierra A, Astha, Merdas K, Chandran N, Ghosh P, Mukherjee S, Bujnicki JM.
Biosci Rep. . 2019
2018
Discovery of selective, orally bioavailable inhibitor of mouse chitotriosidase.
Mazur M, Bartoszewicz A, Dymek B, Salamon M, Andryianau G, Kowalski M, Olejniczak S, Matyszewski K, Pluta E, Borek B, Stefaniak F, Zagozdzon A, Mazurkiewicz M, Koralewski R, Czestkowski W, Piotrowicz M, Niedziejko P, Gruza MM, Dzwonek K, Golebiowski A, Golab J, Olczak J.
28(3). 2018
The OB-fold proteins of the Trypanosoma brucei editosome execute RNA-chaperone activity.
Voigt C, Dobrychlop M, Kruse E, Czerwoniec A, Kasprzak JM, Bytner P, Campo CD, Leeder WM, Bujnicki JM, Göringer HU.
Nucleic Acids Res.. 2018
Positioning Europe for the EPITRANSCRIPTOMICS challenge.
Jantsch MF et al. (Bujnicki J, Purta E)
RNA Biol.. 2018
Human RNA cap1 methyltransferase CMTr1 cooperates with RNA helicase DHX15 to modify RNAs with highly structured 5' termini.
Toczydlowska-Socha D, Zielinska MM, Kurkowska M, Astha, Almeida CF, Stefaniak F, Purta E, Bujnicki JM.
Philos Trans R Soc Lond B Biol Sci.. 2018
Crystal structure of human Acinus RNA recognition motif domain.
Fernandes H, Czapinska H, Grudziaz K, Bujnicki JM, Nowacka M.
PeerJ.. 2018
Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes.
Nithin C, Ghosh P, Bujnicki JM.
Genes (Basel). 2018
Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition.
Kumari P, Aeschimann F, Gaidatzis D, Keusch JJ, Ghosh P, Neagu A, Pachulska-Wieczorek K, Bujnicki JM, Gut H, Großhans H, Ciosk R.
Nat Commun.. 2018
Novel inhibitors of the rRNA ErmC' methyltransferase to block resistance to macrolides, lincosamides, streptogramine B antibiotics.
Foik IP, Tuszynska I, Feder M, Purta E, Stefaniak F, Bujnicki JM.
Eur J Med Chem.. 2018
Antisense and yet sensitive: Copy number control of rolling circle-replicating plasmids by small RNAs.
Pluta R, Espinosa M.
Wiley Interdiscip Rev RNA. 2018
MODOMICS: a database of RNA modification pathways. 2017 update.
Boccaletto P, Machnicka MA, Purta E, Piatkowski P, Baginski B, Wirecki TK, de Crécy-Lagard V, Ross R, Limbach PA, Kotter A, Helm M, Bujnicki JM.
Nucleic Acids Res.. 2018
RNArchitecture: a database and a classification system of RNA families, with a focus on structural information.
Boccaletto P, Magnus M, Almeida C, Zyla A, Astha A, Pluta R, Baginski B, Jankowska E, Dunin-Horkawicz S, Wirecki TK, Boniecki MJ, Stefaniak F, Bujnicki JM.
Nucleic Acids Res.. 2018
2017
Impact of the structural integrity of the three-way junction of adenovirus VAI RNA on PKR inhibition.
Dzananovic E, Astha, Chojnowski G, Deo S, Booy EP, Padilla-Meier P, McEleney K, Bujnicki JM, Patel TR, McKenna SA.
PLoS One. 2017
Occurrence and stability of lone pair-π stacking interactions between ribose and nucleobases in functional RNAs.
Chawla M, Chermak E, Zhang Q, Bujnicki JM, Oliva R, Cavallo L.
Nucleic Acids Res.. 2017
SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments.
Piątkowski P, Jabłońska J, Żyła A, Niedziałek, Matelska D, Jankowska E, Waleń T, Dawson WK, Bujnicki JM.
Nucleic Acids Res.. 2017
Mutations in human AID differentially affect its ability to deaminate cytidine and 5-methylcytidine in ssDNA substrates in vitro
Budzko L, Jackowiak P, Kamel K, Sarzynska J, Bujnicki JM, Figlerowicz M
Sci Rep. 2017
Defining the crucial domain and amino acid residues in bacterial Lon protease for DNA binding and processing of DNA-interacting substrates
Karlowicz A, Wegrzyn K, Gross M, Kaczynska D, Ropelewska M, Siemiątkowska M, Bujnicki JM, Konieczny I
J Biol Chem. 2017
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme
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. 2017
Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering and computational methods
Patel T, Chojnowski G, Astha, Koul A, McKenna S, Bujnicki JM
Methods. 2017
2016
Sequence-specific endoribonucleases.
Głów D, Nowacka M, Skowronek KJ, Bujnicki JM.
Postępy Biochemii. 2016
Coarse-grained modeling of RNA 3D structure
Dawson WK, Maciejczyk M, Jankowska EJ, Bujnicki JM
Methods. 2016
tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs
Machnicka MA, Dunin-Horkawicz S, de Crécy-Lagard V, Bujnicki JM
Methods. 2016
Asymmetric DNA methylation by dimeric EcoP15I DNA methyltransferase
Urulangodi M, Dhanaraju R, Gupta K, Roy RP, Bujnicki JM, Rao DN
Biochimie. 2016
MQAPsingle: A quasi single-model approach for estimation of the quality of individual protein structure models
Pawlowski M, Kozlowski L, Kloczkowski A
Proteins. 2016
Molecularly Imprinted Polymer (MIP) Film with Improved Surface Area Developed by Using Metal-Organic Framework (MOF) for Sensitive Lipocalin (NGAL) Determination.
Iskierko Z, Sharma PS, Prochowicz D, Fronc K, D'Souza F, Toczydłowska D, Stefaniak F, Noworyta K
ACS Appl Mater Interfaces.. 2016
Identification of protein structural elements responsible for the diversity of sequence preferences among Mini-III RNases.
Glow D, Kurkowska M, Czarnecka J, Szczepaniak K, Pianka D, Kappert V, Bujnicki JM, Skowronek KJ
Sci Rep.. 2016
Structural and functional insights into tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue
Van Laer B, Roovers M, Wauters L, Kasprzak JM, Dyzma M, Deyaert E, Singh R, Feller A, Bujnicki JM, Droogmans L, Versées W
Nucleic Acids Res. 2016
Computational modeling of RNA 3D structures and interactions
Dawson WK, Bujnicki JM
Curr Opin Struct Biol. 2016
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction
Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM
Nucleic Acids Res. 2016
The architecture of the Schizosaccharomyces pombe CCR4-NOT complex
Ukleja M, Cuellar J, Siwaszek A, Kasprzak JM, Czarnocki-Cieciura M, Bujnicki JM, Dziembowski A, Valpuesta J
Nature Commun. 2016
Loss of conserved non-coding RNAs in genomes of bacterial endosymbionts
Matelska D, Kurkowska M, Purta E, Bujnicki JM, Dunin-Horkawicz S
Genome Biol Evol. 2016
Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori
Yahara K, Furuta Y, Morimoto S, Kikutake C, Komukai S, Matelska D, Dunin-Horkawicz S, Bujnicki JM, Uchiyama I, Kobayashi I
DNA Res. 2016
SimRNAweb: a web server for RNA 3D structure modeling with optional restraints
Magnus MM, Boniecki MJ, Dawson WK, Bujnicki JM
Nucleic Acids Res.. 2016
2015
Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes.
Machnicka AM, Kaminska KH, Dunin-Horkawicz S, Bujnicki JM.
BMC Bioinformatics. 2015
RNAcentral: a comprehensive database of non-coding RNA sequences
The RNAcentral Consortium (Petrov AI et al within Bujnicki JM)
Nucleic Acids Res. 2015
Magnesium binding architectures in RNA crystal structures: validation binding preferences, classification, and motif detection
Zheng H, Shabalin I, Handing K, Bujnicki JM, Minor M
Nucleic Acids Res. 2015
NPDock – a web server for protein-nucleic acid docking
Tuszynska I, Magnus M, Jonak K, Dawson W, Bujnicki JM
Nucleic Acids Res. 2015
Biochemical Characterization and Validation of a Catalytic Site of a Highly Thermostable Ts2631 Endolysin from the Thermus scotoductus Phage vB_Tsc2631
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
PLoS One. 2015
Computational methods for prediction of RNA interactions with metal ions and small organic ligands
Philips A, Lach G, Bujnicki JM
Methods Enzymol. 2015
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures
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. 2015
A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing
Liu S, Mozaffari-Jovin S, Wollenhaupt J, Santos KF, Theuser M, Dunin-Horkawicz S, Fabrizio P, Bujnicki JM, Lührmann R, Wahl MC
eLife. 2015
Sequence-specific cleavage of dsRNA by Mini-III RNase
Glow D, Pianka D, Sulej A, Kozlowski L, Czarnecka J, Chojnowski G, Skowronek KJ, Bujnicki JM
Nucleic Acids Res. 2015
Characterization of the termini of the West Nile virus genome and their interactions with the small isoform of the 2' 5'-Oligoadenylate Synthetase family
Deo S, Patel TR, Chojnowski G, Koul A, Dzananovic E, McEleney K, Bujnicki JM, McKenna SA
J Struct Biol. 2015
Structure and intrinsic disorder of the proteins of the Trypanosoma brucei editosome
Czerwoniec A, Kasprzak JM, Bytner P, Dobrychlop M, Bujnicki JM
FEBS Lett. 2015
Brickworx builds recurrent RNA and DNA structural motifs into medium and low-resolution electron density maps
Chojnowski G, Walen T, Piatkowski P, Potrzebowski W, Bujnicki JM
Acta Crystallogr D Biol Crystallogr. 2015
An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies
Chawla M, Oliva R, Bujnicki JM, Cavallo L
Nucleic Acids Res. 2015
A magnetic origin of cuprate superconductivity? A MaxEnt-mu SR view
Boekema C, Owens F, Love A, Li Z, Sakkaris P, Dawson WK
Int J Mod Phys B. 2015
The signature of the five-stranded vRRM fold defined by functional, structural and computational analysis of the hnRNP L protein
Blatter M, Dunin-Horkawicz S, Grishina I, Maris C, Thore S, Maier T, Bindereif A, Bujnicki JM, Allain FHT
J Mol Biol. 2015
Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain
Bocian-Ostrzycka KM, Łasica AM, Dunin-Horkawicz S, Grzeszczuk MJ, Drabik K, Dobosz AM, Godlewska R, Nowak E, Collet J-F, Jagusztyn-Krynicka EK
Frontiers in Microbiology. 2015
Helicobacter pylori HP0377, a member of the Dsb family, is an untypical multifunctional CcmG that cooperates with dimeric thioldisulfide oxidase HP0231
Roszczenko P, Grzeszczuk M, Kobierecka P, Wywial E, Urbanowicz P, Wincek P, Nowak E, Jagusztyn-Krynicka EK
BMC Microbiol.. 2015
2014
Distribution and frequencies of post-transcriptional modifications in tRNAs.
Machnicka M, Olchowik A, Grosjean H, Bujnicki JM.
RNA Biol.. 2014
RNA methyltransferases involved in 5' cap biosynthesis.
Byszewska M, Smietanski M, Purta E, Bujnicki JM.
RNA Biol.. 2014
Designability landscape reveals sequence features that define axial helix rotation in four-helical homo-oligomeric antiparallel coiled-coil structures
Szczepaniak K, Lach G, Bujnicki JM, Dunin-Horkawicz S
J Struct Biol.. 2014
Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA
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
PLoS One.. 2014
ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes
Walen T, Chojnowski G, Gierski P,Bujnicki JM,
Nucleic Acids Res.. 2014
Structural and degradative aspects of ornithine decarboxylase antizyme inhibitor 2
Ramos-Molina B, Lambertos A, Lopez-Contreras AJ, Kasprzak JM, Czerwoniec A, Bujnicki JM, Cremades A, Penafiel R
FEBS Open Bio.. 2014
Female-specific gene expression in dioecious liverwort Pellia endiviifolia is developmentally regulated and connected to archegonia production
Sierocka I, Kozlowski LP, Bujnicki JM, Jarmolowski A, Szweykowska-Kulinska Z
BMC Plant Biol.. 2014
Computational modeling of RNA 3D structures, with the aid of experimental restraints
Magnus M, Matelska D, Lach G, Chojnowski G, Boniecki MJ, Purta E, Dawson W, Dunin-Horkawicz S, Bujnicki JM
RNA Biol.. 2014
Automated modeling of RNA 3D structure
Rother K, Rother M, Skiba P, Bujnicki JM
Methods Mol Biol. 2014
Structural basis of the methylation specificity of R.DpnI
Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler M
Nucleic Acids Res.. 2014
The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification
Majorek KA, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A, Nowotny M, Ginalski K, Bujnicki JM
Nucleic Acids Res.. 2014
Potassium channel in the mitochondria of human keratinocytes
Toczyłowska-Mamińska R, Olszewska A, Laskowski M, Bednarczyk P, Skowronek K, Szewczyk A
J Invest Dermatol. 2014
Labeling of platelet-derived growth factor by reversible biotinylation to visualize its endocytosis by microscopy
Sadowski Ł, Jastrzębski K, Purta E, Hellberg C, Miaczynska M
Methods Enzymol.. 2014
New simple efficient algorithms computing powers and runs in strings
Crochemore M, Iliopoulos CS, Kubica M, Radoszewski J, Rytter W, Stencel K, Walen T
Discrete Applied Mathematics. 2014
Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation
Smietanski M, Werner M, Purta E, Kaminska KH, Stepinski J, Darzynkiewicz E, Nowotny M, Bujnicki JM
Nat Commun. 2014
RNA Bricks - a database of RNA 3D motifs and their interactions
Chojnowski G, Walen T, Bujnicki JM
Nucleic Acids Res.. 2014
Solution conformation of Adenovirus Virus Associated RNA-I and its interaction with PKR
Dzananovic E, Patel TR, Chojnowski G, Boniecki MJ, Deo S, McEleney K, Harding SE, Bujnicki JM, McKenna SA
J Struct Biol. 2014
Novel Highly Thermostable Endolysin from Thermus scotoductus MAT2119 Bacteriophage Ph2119 with Amino Acid Sequence Similarity to Eukaryotic Peptidoglycan Recognition Proteins
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
Appl Environ Microbiol. 2014
Computational modeling of protein-RNA complex structures
Tuszynska I, Matelska D, Magnus M, Chojnowski G, Kasprzak JM, Kozlowski LP, Dunin-Horkawicz S, Bujnicki JM
Methods. 2014
2013
Rational design of helical nanotubes from self-assembly of coiled-coil lock washers
Xu C, Liu R, Mehta AK, Guerrero-Ferreira RC, Wright ER, Dunin-Horkawicz S, Morris K, Serpell LC, Zuo X, Wall JS, Conticello VP
J Am Chem Soc.. 2013
LigandRNA: computational predictor of RNA-ligand interactions
Philips A, Milanowska K, Lach G, Bujnicki JM
RNA. 2013
Caveolin-1 - a novel interacting partner of organic cation/carnitine transporter (octn2): effect of protein kinase C on this interaction in rat astrocytes.
Czeredys M, Samluk L, Michalec K, Tułodziecka K, Skowronek K, Nałęcz KA
PLoS One. 2013
S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA
Matelska D, Purta E, Panek S, Boniecki MJ, Bujnicki JM, Dunin-Horkawicz S
RNA. 2013
A linear time algorithm for consecutive permutation pattern matching
Kubica M, Kulczyńskia T, Radoszewskia J, Rytter W,Walen T
Information Processing Letters. 2013
Putative Structural and Functional Coupling of the Mitochondrial BKCa Channel to the Respiratory Chain
Bednarczyk P, Wieckowski MR, Broszkiewicz M, Skowronek K, Siemen D, Szewczyk A
PLoS One. 2013
A note on efficient computation of all Abelian periods in a string
Crochemore M, Iliopoulos C.S, Kociumaka T, Kubica M, Pachocki J, Radoszewski J, Rytter W,Tyczyński W, Waleń T
Information Processing Letters. 2013
QA-RecombineIt: a server for quality assessment and recombination of protein models
Pawlowski M, Bogdanowicz A, Bujnicki JM
Nucleic Acids Res. 2013
RNAlyzer--novel approach for quality analysis of RNA structural models
Lukasiak P, Antczak M, Ratajczak T, Bujnicki JM, Szachniuk M, Adamiak RW, Popenda M, Blazewicz J
Nucleic Acids Res. 2013
CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction
Puton T, Kozlowski LP, Rother KM, Bujnicki JM
Nucleic Acids Res.. 2013
Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid
Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M
Nucleic Acids Res. 2013
RNApathwaysDB – a database of RNA maturation and decay pathways
Milanowska K, Mikolajczak K, Lukasik A, Skorupski M, Balcer Z, Machnicka MA, Nowacka M, Rother KM, Bujnicki JM
Nucleic Acids Res. 2013
MODOMICS: a database of RNA modification pathways: 2013 update
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
Nucleic Acids Res. 2013
2012
Structure prediction of alternatively spliced proteins In „Alternative pre-mRNA Splicing: Theory and Protocols: The Complete Guide for Biomedical Scientists”
Kozlowski L, Orlowski J, Bujnicki JM
. 2012
Template-based and template-free modeling of RNA 3D structure: inspirations from protein structure modeling.
Rother K, Rother M, Boniecki M, Puton T, Tomala K, Lukasz P, Bujnicki JM.
RNA 3D Structure Analysis and Prediction. 2012
MetaDisorder: A meta-server for the prediction of intrinsic disorder in proteins
Kozlowski LP, Bujnicki JM
BMC Bioinformatics. 2012
Molecular evolution of dihydrouridine synthases
Kasprzak JM, Czerwoniec A, Bujnicki JM
BMC Bioinformatics. 2012
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
Kusio-Kobialka M, Wolanin K, Podszywalow-Bartnicka P, Sikora E, Skowronek K, McKenna SL, Ghizzoni M, Dekker FJ, Piwocka K
Apoptosis. 2012
A novel insight into the oxidoreductase activity of Helicobacter pylori HP0231 protein
Roszczenko P, Radomska KA, Wywial E, Collet JF, Jagusztyn-Krynicka EK
PLoS One. 2012
A novel homozygous p.Arg527Leu LMNA mutation in two unrelated egyptian families causes overlapping mandibuloacral dysplasia and progeria syndrome
Al-Haggar M, Madej-Pilarczyk A, Kozlowski L, Bujnicki JM, Yahia S, Abdel-Hadi D, Shams A, Ahmad N, Hamed S, Puzianowska-Kuznicka M
Eur J Hum Genet. 2012
MetaLocGramN: A meta-predictor of protein subcellular localization for Gram-negative bacteria
Magnus M, Pawlowski M, Bujnicki JM
Biochim Biophys Acta. 2012
Rational engineering of sequence specificity in R.MwoI restriction endonuclease
Skowronek K, Boniecki MJ, Kluge B, Bujnicki JM
Nucleic Acids Res. 2012
Delineation of structural domains and identification of functionally important residues in DNA repair enzyme Exonuclease VII
Poleszak K, Kaminska KH, Dunin-Horkawicz S, Lupas A, Skowronek KJ, Bujnicki JM
Nucleic Acids Res. 2012
Structural bioinformatics of the human spliceosomal proteome
Korneta I, Magnus M, Bujnicki JM
Nucleic Acids Res. 2012
Novel non-specific DNA adenine methyltransferases
Drozdz M, Piekarowicz A, Bujnicki JM, Radlinska M
Nucleic Acids Res. 2012
Sequence-specific cleavage of the RNA strand in DNA-RNA hybrids by the fusion of ribonuclease H with a zinc finger
Sulej AA, Tuszynska I, Skowronek KJ, Nowotny M, Bujnicki JM
Nucleic Acids Res. 2012
The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement
Pawlowski M, Bujnicki JM
BMC Bioinformatics. 2012
RNAmap2D -- calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures
Pietal MJ, Szostak N, Rother KM, Bujnicki JM
BMC Bioinformatics. 2012
Crystal structure and mechanism of action of the N6-methyladenine dependent type IIM restriction endonuclease
Siwek W, Czapinska H, Bochtler M, Bujnicki JM, Skowronek K
Nucleic Acids Res. 2012
Protein kinase C regulates amino acid transporter ATB
Samluk L, Czeredys M, Skowronek K, Nałęcz KA
Biochem Biophys Res Commun.. 2012
Statins Impair Glucose Uptake in Tumor Cells
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
Neoplasia. 2012
Einstein–Hopf drag, Doppler shift of thermal radiation and blackbody drag: Three perspectives on quantum friction
Lach G, DeKievet M, Jentschura UD
Cent. Eur. J. Phys.. 2012
Crystal structures of the tRNA:m(2)G6 methyltransferase Trm14/TrmN from two domains of life
Fislage M, Roovers M, Tuszynska I, Bujnicki JM, Droogmans L, Versées W
Nucleic Acids Res. 2012
RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction
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. 2012
RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes
Chojnowski G, Bujnicki JM, Bochtler M
Bioinformatics. 2012
Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities
Zylicz-Stachula A, Zolnierkiewicz O, Lubys A, Ramanauskaite D, Mitkaite G, Bujnicki JM, Skowron P
BMC Mol Biol. 2012
The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N2-methylguanosine at position 6 in tRNA
Roovers M, Oudjama Y, Fislage M, Bujnicki JM, Versées W, Droogmans L
RNA. 2012
Crohn's Disease Risk Alleles on the NOD2 Locus Have Been Maintained by Natural Selection on Standing Variation
Nakagome S, Mano S, Kozlowski L, Bujnicki JM, Shibata H, Fukumaki Y, Kidd JR, Kidd KK, Kawamura S, Oota H
Mol Biol Evol. 2012
Computational methods for prediction of protein-RNA interactions
Puton T, Kozlowski L, Tuszynska I, Rother K, Bujnicki JM
J Struct Biol. 2012
A toolbox for developing bioinformatics software
Rother K, Potrzebowski W, Puton T, Rother M, Wywial E, Bujnicki JM
Brief Bioinform. 2012
Structure and operation of the DNA-translocating type I DNA restriction enzymes
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
Genes Dev. 2012
MetalionRNA: computational predictor of metal-binding sites in RNA structures
Philips A, Milanowska K, Lach G, Boniecki M, Rother K, Bujnicki JM
Bioinformatics. 2012
2011
Virtual screening strategies in drug design - methods and applications
Bielska E, Lucas X, Czerwoniec A, Kasprzak JM, Kaminska KH, Bujnicki JM
BioTechnologia. 2011
STAT1 as a novel therapeutical target in pro-atherogenic signal integration of IFNg, TLR4 and IL-6 in vascular disease
Sikorski K, Czerwoniec A, Bujnicki JM, Wesoly J, Bluyssen HAR
Cytokine Growth Factor Rev.. 2011
RNA tertiary structure prediction with ModeRNA
Rother M, Rother K, Puton T, Bujnicki JM
Brief Bioinform. 2011
Databases and bioinformatics tools for the study of DNA repair
Milanowska K, Rother K, Bujnicki JM
Mol Biol Int. 2011
Effect of substrate features and mutagenesis of active site tyrosine residues on the reaction course catalysed by Trypanosoma brucei sterol C-24-methyltransferase
Liu J, Ganapathy K, Wywial E, Bujnicki JM, Nwogwugwu CA, Nes WD
Biochem J. 2011
Identification and modeling of a phosphatase-like domain in a tRNA 2'-O-ribosyl phosphate transferase Rit1p
Czerwoniec A, Bujnicki JM
Cell Cycle. 2011
RNAcentral: A vision for an international database of RNA sequences
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
RNA. 2011
ModeRNA: a tool for comparative modeling of RNA 3D structure
Rother M, Rother K, Puton T, Bujnicki JM
Nucleic Acids Res. 2011
2'-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family
Werner M, Purta E, Kaminska KH, Cymerman IA, Campbell DA, Mittra B, Zamudio JR, Sturm NR, Jaworski J, Bujnicki JM
Nucleic Acids Res. 2011
DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking
Tuszynska I, Bujnicki JM
BMC Bioinformatics. 2011
ModeRNA server: an online tool for modeling RNA 3D structures
Rother M, Milanowska K, Puton T, Jeleniewicz J, Rother K, Bujnicki JM
Bioinformatics. 2011
RNA and protein 3D structure modeling: similarities and differences
Rother K, Rother M, Boniecki M, Puton T, Bujnicki JM
J Mol Model.. 2011
A single zinc ion is sufficient for an active Trypanosoma brucei tRNA editing deaminase
Spears JL, Rubio MA, Gaston KW, Wywial E, Strikoudis A, Bujnicki JM, Papavasiliou FN, Alfonzo JD
J Biol Chem. 2011
Evidence for an evolutionary antagonism between Mrr and Type III modification systems.
Tesfazgi Mebrhatu M, Wywial E, Ghosh A, Michiels CW, Lindner AB, Taddei F, Bujnicki JM, Van Melderen L, Aertsen A
Nucleic Acids Res. 2011
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
Husain N, Obranic S, Koscinski L, Seetharaman J, Babic F, Bujnicki JM, Maravic-Vlahovicek G, Sivaraman J
Nucleic Acids Res. 2011
"4D Biology for health and disease" workshop report
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
N Biotechnol. 2011
REPAIRtoire-a database of DNA repair pathways
Milanowska K, Krwawicz J, Papaj G, Kosinski J, Poleszak K, Lesiak J, Osinska E, Rother K, Bujnicki JM
Nucleic Acids Res. 2011
2010
BioCatalogue: a universal catalogue of web services for the life sciences
Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA
Nucleic Acids Res. 2010
Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site
Tkaczuk KL
J Mol Model.. 2010
IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities
Rother K, Hoffmann S, Bulik S, Hoppe A, Gasteiger J, Holzhütter HG
Biophys J.. 2010
A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI).
Khan F, Furuta Y, Kawai M, Kaminska KH, Ishikawa K, Bujnicki JM, Kobayashi I
Nucleic Acids Res. 2010
Predicting atomic details of the unfolding pathway for YibK, a knotted protein from the SPOUT superfamily
Tuszynska I, Bujnicki JM
J Biomol Struct Dyn. 2010
Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria.
Kaminska KH, Purta E, Hansen LH, Bujnicki JM, Vester B, Long KS
Nucleic Acids Res. 2010
The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket.
Zhou X, Chua TK, Tkaczuk KL, Bujnicki JM, Sivaraman J
J Struct Biol. 2010
Physiological truncation and domain organization of a novel uracil-DNA-degrading factor.
Pukáncsik M, Békési A, Klement E, Hunyadi-Gulyás E, Medzihradszky KF, Kosinski J, Bujnicki JM, Alfonso C, Rivas G, Vértessy BG
FEBS J. 2010
The YTH domain is a novel RNA binding domain.
Zhang Z, Theler D, Kaminska KH, Hiller M, de la Grange P, Pudimat R, Rafalska I, Heinrich B, Bujnicki JM, Allain FH, Stamm S
J Biol Chem. 2010
Co-evolution-driven switch of J-protein specificity towards an Hsp70 partner.
Pukszta S, Schilke B, Dutkiewicz R, Kominek J, Moczulska K, Stepien B, Reitenga KG, Bujnicki JM, Williams B, Craig EA, Marszalek J
EMBO Rep. 2010
New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA.
Kempenaers M, Roovers M, Oudjama Y, Tkaczuk KL, Bujnicki JM, Droogmans L
Nucleic Acids Res. 2010
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.
Husain N, Tkaczuk KL, Tulsidas SR, Kaminska KH, Cubrilo S, Maravić-Vlahovicek G, Bujnicki JM, Sivaraman J
Nucleic Acids Res. 2010
Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair.
Kosinski J, Hinrichsen I, Bujnicki JM, Friedhoff P, Plotz G
Hum Mutat. 2010
Crystal structure of a fructokinase homolog from Halothermothrix orenii
Chua TK, Seetharaman J, Kasprzak JM, Ng C, Patel BK, Love C, Bujnicki JM, Sivaraman J
J Struct Biol. 2010
FILTREST3D: discrimination of structural models using restraints from experimental data.
Gajda MJ, Tuszynska I, Kaczor M, Bakulina AY, Bujnicki JM
Bioinformatics. 2010
2009
Modeling of Escherichia coli Endonuclease V structure in complex with DNA.
Majorek KA, Bujnicki JM
J Mol Model. 2009
The mitotic kinesin-14 Ncd drives directional microtubule-microtubule sliding.
Fink G, Hajdo L, Skowronek KJ, Reuther C, Kasprzak AA, Diez S
Nat Cell Biol. 2009
MODOMICS: a database of RNA modification pathways. 2008 update
Czerwoniec A, Dunin-Horkawicz S, Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Grosjean H, Rother K
Nucleic Acids Res. 2009
Functional analysis of MmeI from methanol utilizer Methylophilus methylotrophus, a subtype IIC restriction-modification enzyme related to type I enzymes.
Nakonieczna J, Kaczorowski T, Obarska-Kosinska A, Bujnicki JM
Appl Environ Microbiol. 2009
The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein
Kennaway CK, Obarska-Kosinska A, White JH, Tuszynska I, Cooper LP, Bujnicki JM, Trinick J, Dryden DT
Nucleic Acids Res. 2009
Conformation of a plasmid replication initiator protein affects its proteolysis by ClpXP system
Pierechod M, Nowak A, Saari A, Purta E, Bujnicki JM, Konieczny I
Protein Sci. 2009
Medaka: a promising model animal for comparative population genomics.
Matsumoto Y, Oota H, Asaoka Y, Nishina H, Watanabe K, Bujnicki JM, Oda S, Kawamura S, Mitani H
BMC Res Notes. 2009
Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors
Bauer RA, Rother K, Moor P, Reinert K, Steinke T, Bujnicki JM
Algorithms. 2009
YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA.
Purta E, O'Connor M, Bujnicki JM, Douthwaite S
Mol Microbiol. 2009
AAN82231 protein from uropathogenic E. coli CFT073 is a close paralog of DsbB enzymes and does not belong to the DsbI family
Pawłowski M, Lasica AM, Jagusztyn-Krynicka EK, Bujnicki JM
Pol J Microbiol. 2009
Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family.
Zylicz-Stachula A, Bujnicki JM, Skowron PM
BMC Mol Biol. 2009
SMN-assisted assembly of snRNP-specific Sm cores in trypanosomes.
Palfi Z, Jaé N, Preusser C, Kaminska KH, Bujnicki JM, Lee JH, Günzl A, Kambach C, Urlaub H, Bindereif A
Genes Dev. 2009
Common design principles in the spliceosomal RNA helicase Brr2 and in the Hel308 DNA helicase.
Pena V, Jovin SM, Fabrizio P, Orlowski J, Bujnicki JM, Lührmann R, Wahl MC
Mol Cell. 2009
Integrating ELF4 into the circadian system through combined structural and functional studies.
Kolmos E, Nowak M, Werner M, Fischer K, Schwarz G, Mathews S, Schoof H, Nagy F, Bujnicki JM, Davis SJ
HFSP J. 2009
Identification and classification of bcl genes and proteins of Bacillus cereus group organisms and their application in Bacillus anthracis detection and fingerprinting.
Leski TA, Caswell CC, Pawlowski M, Klinke DJ, Bujnicki JM, Hart SJ, Lukomski S
Appl Environ Microbiol. 2009
2008
Modeling and experimental analyses reveal a two-domain structure and amino acids important for the activity of aminoglycoside resistance methyltransferase Sgm.
Maravić Vlahovicek G, Cubrilo S, Tkaczuk KL, Bujnicki JM
Biochim Biophys Acta. 2008
Structural integrity of the beta beta alpha-Metal finger motif is required for DNA binding and stable protein-DNA complex formation in R.KpnI.
Vasu K, Saravanan M, Bujnicki JM, Nagaraja V
Biochim Biophys Acta. 2008
Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms(2)io(6)A37 in tRNA.
Kaminska KH, Baraniak U, Boniecki M, Nowaczyk K, Czerwoniec A, Bujnicki JM
Proteins. 2008
Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA.
Roovers M, Oudjama Y, Kaminska KH, Purta E, Caillet J, Droogmans L, Bujnicki JM
Proteins. 2008
Bacteriophage Mu Mom protein responsible for DNA modification is a new member of the acyltransferase superfamily.
Kaminska KH, Bujnicki JM
Cell Cycle. 2008
The TbMTr1 spliced leader RNA cap 1 2'-O-ribose methyltransferase from Trypanosoma brucei acts with substrate specificity
Mittra B, Zamudio JR, Bujnicki JM, Stepinski J, Darzynkiewicz E, Campbell DA, Sturm NR
J Biol Chem. 2008
Virtual screening and experimental verification to identify potential inhibitors of the ErmC methyltransferase responsible for bacterial resistance against macrolide antibiotics.
Feder M, Purta E, Koscinski L, Cubrilo S, Maravic Vlahovicek G, Bujnicki JM
ChemMedChem. 2008
EXOG, a novel paralog of Endonuclease G in higher eukaryotes.
Cymerman IA, Chung I, Beckmann BM, Bujnicki JM, Meiss G
Nucleic Acids Res. 2008
Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA.
Sen TZ, Kloster M, Jernigan RL, Kolinski A, Bujnicki JM, Kloczkowski A
Biophys J. 2008
The structure of sucrose phosphate synthase from Halothermothrix orenii reveals its mechanism of action and binding mode.
Chua TK, Bujnicki JM, Tan TC, Huynh F, Patel BK, Sivaraman J
Plant Cell. 2008
The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK).
Roovers M, Kaminska KH, Tkaczuk KL, Gigot D, Droogmans L, Bujnicki JM
Nucleic Acids Res. 2008
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.
Orlowski J, Bujnicki JM
Nucleic Acids Res. 2008
Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits.
White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM, Johnson AW
Mol Cell Biol. 2008
The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family.
Kosinski J, Plotz G, Guarné A, Bujnicki JM, Friedhoff P
J Mol Biol. 2008
YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA.
Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Douthwaite S
RNA. 2008
MetaMQAP: a meta-server for the quality assessment of protein models.
Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM
BMC Bioinformatics. 2008
Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes.
Sunita S, Tkaczuk KL, Purta E, Kasprzak JM, Douthwaite S, Bujnicki JM, Sivaraman J
J Mol Biol. 2008
HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling.
Obarska-Kosinska A, Taylor JE, Callow P, Orlowski J, Bujnicki JM, Kneale GG
J Mol Biol. 2008
YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962
Purta E, O\'Connor M, Bujnicki JM, Douthwaite S
J Mol Biol. 2008
IAPs contain an evolutionarily conserved ubiquitin-binding domain that regulates NF-kappaB as well as cell survival and oncogenesis.
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
Nat Cell Biol. 2008
Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr.
Orlowski J, Mebrhatu MT, Michiels CW, Bujnicki JM, Aertsen A
Biochem Biophys Res Commun. 2008
2007
The 2'-O-ribose methyltransferase for cap 1 of spliced leader RNA and U1 small nuclear RNA in Trypanosoma brucei
Zamudio JR, Mittra B, Foldynová-Trantírková S, Zeiner GM, Lukes J, Bujnicki JM, Sturm NR, Campbell DA
Mol Cell Biol. 2007
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.
Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM
BMC Bioinformatics. 2007
Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC.
Sunita S, Purta E, Durawa M, Tkaczuk KL, Swaathi J, Bujnicki JM, Sivaraman J
Nucleic Acids Res. 2007
Human lysosomal DNase IIalpha contains two requisite PLD-signature (HxK) motifs: evidence for a pseudodimeric structure of the active enzyme species.
Schäfer P, Cymerman IA, Bujnicki JM, Meiss G
Protein Sci. 2007
SURF'S UP! - protein classification by surface comparisons
Sasin JM, Godzik A, Bujnicki JM
J Biosci. 2007
Transcriptome profile of human colorectal adenomas.
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
Mol Cancer Res. 2007
PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure.
Pietal MJ, Tuszynska I, Bujnicki JM
Bioinformatics. 2007
Structure of a multipartite protein-protein interaction domain in splicing factor prp8 and its link to retinitis pigmentosa.
Pena V, Liu S, Bujnicki JM, Lührmann R, Wahl MC
Mol Cell. 2007
Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding.
Ozanick SG, Bujnicki JM, Sem DS, Anderson JT
Nucleic Acids Res. 2007
I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition
Orlowski J, Boniecki M, Bujnicki JM
Bioinformatics. 2007
Novel protein fold discovered in the PabI family of restriction enzymes.
Miyazono K, Watanabe M, Kosinski J, Ishikawa K, Kamo M, Sawasaki T, Nagata K, Bujnicki JM, Endo Y, Tanokura M, Kobayashi I
Nucleic Acids Res. 2007
Structure and evolutionary origin of Ca(2+)-dependent herring type II antifreeze protein.
Liu Y, Li Z, Lin Q, Kosinski J, Seetharaman J, Bujnicki JM, Sivaraman J, Hew CL
PLoS One. 2007
[Probing of contacts between EcoRII DNA methyltransferase and DNA using substrate analogs and molecular modeling].
Kudan EV, Brevnov MG, Subach OM, Rechkoblit OA, Buĭnitskiĭ IaM, Gromova ES
Mol Biol (Mosk). 2007
A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering.
Kosinski J, Kubareva E, Bujnicki JM
Proteins. 2007
Identification of a missing sequence and functionally important residues of 16S rRNA:m(1)A1408 methyltransferase KamB that causes bacterial resistance to aminoglycoside antibiotics.
Koscinski L, Feder M, Bujnicki JM
Cell Cycle. 2007
Identification of a single HNH active site in type IIS restriction endonuclease Eco31I
Jakubauskas A, Giedriene J, Bujnicki JM, Janulaitis A
J Mol Biol. 2007
Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily.
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
BMC Struct Biol. 2007
Phylogenetic analysis of haloalkane dehalogenases.
Chovancová E, Kosinski J, Bujnicki JM, Damborský J
Proteins. 2007
2006
Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase.
Zegers I, Gigot D, van Vliet F, Tricot C, Aymerich S, Bujnicki JM, Kosinski J, Droogmans L
Nucleic Acids Res. 2006
Complete cap 4 formation is not required for viability in Trypanosoma brucei.
Zamudio JR, Mittra B, Zeiner GM, Feder M, Bujnicki JM, Sturm NR, Campbell DA
Eukaryot Cell. 2006
Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis.
Tkaczuk KL, Obarska A, Bujnicki JM
BMC Evol Biol. 2006
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
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
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
2005
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
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
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
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
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
2004
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
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
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
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
2003
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
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
2002
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
2001
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
Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles.
Bujnicki JM, Rychlewski L
J Mol Microbiol Biotechnol. 2001
Reassignment of specificities of two cap methyltransferase domains in the reovirus lambda 2 protein
Bujnicki JM, Rychlewski L
Genome Biol. 2001
Unusual evolutionary history of the tRNA splicing endonuclease EndA: relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases.
Bujnicki JM, Rychlewski L
Protein Sci. 2001
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
Bujnicki JM, Rychlewski L
Gene. 2001
Sequence analysis and structure prediction of aminoglycoside-resistance 16S rRNA:m7G methyltransferases
Bujnicki JM, Rychlewski L
Acta Microbiol Pol. 2001
Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics.
Bujnicki JM, Rotkiewicz P, Kolinski A, Rychlewski L
Protein Eng. 2001
Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage
Bujnicki JM, Radlinska M, Zaleski P, Piekarowicz A
Acta Biochim Pol. 2001
Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed
Bujnicki JM, Radlinska M, Rychlewski L
Trends Biochem Sci. 2001
Cloning and characterization of M.LmoA118I, a novel DNA:m4C methyltransferase from the Listeria monocytogenes phage A118, a close homolog of M.NgoMXV
Bujnicki JM, Radlinska M
Acta Microbiol Pol. 2001
mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships
Bujnicki JM, Feder M, Radlinska M, Rychlewski L
BMC Bioinformatics. 2001
LiveBench-2: large-scale automated evaluation of protein structure prediction servers.
Bujnicki JM, Elofsson A, Fischer D, Rychlewski L
Proteins. 2001
LiveBench-1: continuous benchmarking of protein structure prediction servers
Bujnicki JM, Elofsson A, Fischer D, Rychlewski L
Protein Sci. 2001
Structure prediction meta server
Bujnicki JM, Elofsson A, Fischer D, Rychlewski L
Bioinformatics. 2001
A model of structure and action of Sau3AI restriction endonuclease that comprises two MutH-like endonuclease domains within a single polypeptide.
Bujnicki JM
Acta Microbiol Pol. 2001
Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons.
Bujnicki JM
Acta Biochim Pol. 2001
In silico analysis of the tRNA:m1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea
Bujnicki JM
FEBS Lett. 2001
2000
Prediction of a common fold for all four subunits of the yeast tRNA splicing endonuclease: implications for the evolution of the EndA/Sen family.
Bujnicki JM, Rychlewski L
FEBS Lett. 2000
Prediction of a novel RNA 2'-O-ribose methyltransferase subfamily encoded by the Escherichia coli YgdE open reading frame and its orthologs
Bujnicki JM, Rychlewski L
Acta Microbiol Pol. 2000
Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc finger and structural similarity to betabetaalphaMe endonucleases
Bujnicki JM, Radlinska M, Rychlewski L
Mol Microbiol. 2000