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

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

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

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

Protein-RNA Docking Benchmark v3.0 Integrated With Binding Affinity.

Kant S, Nithin C, Mukherjee S, Maity A, Bahadur RP.

Proteins. 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

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

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

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

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

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

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

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

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

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

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

Role of Non-Canonical Stacking Interactions of Heterocyclic RNA Bases in Ribosome Function.

Metelev VG, Baulin EF, Bogdanov AA.

Biochemistry (Mosc). 2024

1D2DSimScore: A novel method for comparing contacts in biomacromolecules and their complexes.

Moafinejad SN, Pandaranadar Jeyeram IPN, Jaryani F, Shirvanizadeh N, Baulin EF, Bujnicki JM.

Protein Sci.. 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

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

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

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

Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing.

Luo BN et al. with Bujnicki JM.

Nature Catalysis. 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

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 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

SQUARNA - an RNA secondary structure prediction method based on a greedy stem formation model.

Bohdan DR, Nikolaev GI, Bujnicki JM, Baulin EF

bioRxiv. 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

MODOMICS: a database of RNA modification pathways. 2021 update.

Boccaletto P, Stefaniak F, Ray A, Cappannini A, Mukherjee S, Purta E, Kurkowska M, Shirvanizadeh N, Destefanis E, Groza P, Avşar G, Romitelli A, Pir P, Dassi E, Conticello SG, Aguilo F, Bujnicki JM.

Nucleic Acids Res. 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

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

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

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

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

DNAmoreDB, a database of DNAzymes.

Ponce-Salvatierra A, Boccaletto P, Bujnicki JM.

Nucleic Acids Res.. 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

AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses.

Stefaniak F, Bujnicki JM.

PLoS Comput Biol.. 2021

Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA.

Wegrzyn K, Zabrocka E, Bury K, Tomiczek B, Wieczor M, Czub J, Uciechowska U, Moreno-Del Alamo M, Walkow U, Grochowina I, Dutkiewicz R, Bujnicki JM, Giraldo R, Konieczny I.

Nucleic Acids Res.. 2021

Constrained peptides mimic a viral suppressor of RNA silencing.

Kuepper A, McLoughlin NM, Neubacher S, Yeste-Vázquez A, Collado Camps E, Nithin C, Mukherjee S, Bethge L, Bujnicki JM, Brock R, Heinrichs S, Grossmann TN.

Nucleic Acids Res. . 2021

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

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

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 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

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

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

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

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

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

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

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

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

RNA 3D structure prediction guided by independent folding of homologous sequences.

Magnus M, Kappel K, Das R, Bujnicki JM

BMC Bioinformatics. 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

RNAcentral: a hub of information for non-coding RNA sequences.

The RNAcentral Consortium (Bujnicki JM, Boccaletto P)

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

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

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

Improving selectivity of DNA-RNA binding zinc finger using directed evolution.

Sulej AA

BMC Res Notes. . 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

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

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

Antisense and yet sensitive: Copy number control of rolling circle-replicating plasmids by small RNAs.

Pluta R, Espinosa M.

Wiley Interdiscip Rev RNA. 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

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

Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes.

Nithin C, Ghosh P, Bujnicki JM.

Genes (Basel). 2018

Crystal structure of human Acinus RNA recognition motif domain.

Fernandes H, Czapinska H, Grudziaz K, Bujnicki JM, Nowacka M.

PeerJ.. 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

Positioning Europe for the EPITRANSCRIPTOMICS challenge.

Jantsch MF et al. (Bujnicki J, Purta E)

RNA Biol.. 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

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

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

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

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

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

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

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

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

SimRNAweb: a web server for RNA 3D structure modeling with optional restraints

Magnus MM, Boniecki MJ, Dawson WK, Bujnicki JM

Nucleic Acids Res.. 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

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

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

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

Computational modeling of RNA 3D structures and interactions

Dawson WK, Bujnicki JM

Curr Opin Struct Biol. 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

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

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

MQAPsingle: A quasi single-model approach for estimation of the quality of individual protein structure models

Pawlowski M, Kozlowski L, Kloczkowski A

Proteins. 2016

Asymmetric DNA methylation by dimeric EcoP15I DNA methyltransferase

Urulangodi M, Dhanaraju R, Gupta K, Roy RP, Bujnicki JM, Rao DN

Biochimie. 2016

tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs

Machnicka MA, Dunin-Horkawicz S, de Crécy-Lagard V, Bujnicki JM

Methods. 2016

Coarse-grained modeling of RNA 3D structure

Dawson WK, Maciejczyk M, Jankowska EJ, Bujnicki JM

Methods. 2016

Sequence-specific endoribonucleases.

Głów D, Nowacka M, Skowronek KJ, Bujnicki JM.

Postępy Biochemii. 2016

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

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

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

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

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

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

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

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

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

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

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

Computational methods for prediction of RNA interactions with metal ions and small organic ligands

Philips A, Lach G, Bujnicki JM

Methods Enzymol. 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

NPDock – a web server for protein-nucleic acid docking

Tuszynska I, Magnus M, Jonak K, Dawson W, 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

RNAcentral: a comprehensive database of non-coding RNA sequences

The RNAcentral Consortium (Petrov AI et al within Bujnicki JM)

Nucleic Acids Res. 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

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

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

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

RNA Bricks - a database of RNA 3D motifs and their interactions

Chojnowski G, Walen T, Bujnicki JM

Nucleic Acids Res.. 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

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

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

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

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

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

Automated modeling of RNA 3D structure

Rother K, Rother M, Skiba P, Bujnicki JM

Methods Mol 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

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

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

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

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

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

RNA methyltransferases involved in 5' cap biosynthesis.

Byszewska M, Smietanski M, Purta E, Bujnicki JM.

RNA Biol.. 2014

Distribution and frequencies of post-transcriptional modifications in tRNAs.

Machnicka M, Olchowik A, Grosjean H, Bujnicki JM.

RNA Biol.. 2014

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

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

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

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

Bioinformatics and computational biology in Poland

Bujnicki JM, Tiuryn J

PLoS Comput Biol. 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

QA-RecombineIt: a server for quality assessment and recombination of protein models

Pawlowski M, Bogdanowicz A, Bujnicki JM

Nucleic Acids Res. 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

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 linear time algorithm for consecutive permutation pattern matching

Kubica M, Kulczyńskia T, Radoszewskia J, Rytter W,Walen T

Information Processing Letters. 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

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

LigandRNA: computational predictor of RNA-ligand interactions

Philips A, Milanowska K, Lach G, Bujnicki JM

RNA. 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

MetalionRNA: computational predictor of metal-binding sites in RNA structures

Philips A, Milanowska K, Lach G, Boniecki M, Rother K, Bujnicki JM

Bioinformatics. 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

A toolbox for developing bioinformatics software

Rother K, Potrzebowski W, Puton T, Rother M, Wywial E, Bujnicki JM

Brief Bioinform. 2012

Computational methods for prediction of protein-RNA interactions

Puton T, Kozlowski L, Tuszynska I, Rother K, Bujnicki JM

J Struct Biol. 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

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

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

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

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

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

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

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

Protein kinase C regulates amino acid transporter ATB

Samluk L, Czeredys M, Skowronek K, Nałęcz KA

Biochem Biophys Res Commun.. 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

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

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

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

Novel non-specific DNA adenine methyltransferases

Drozdz M, Piekarowicz A, Bujnicki JM, Radlinska M

Nucleic Acids Res. 2012

Structural bioinformatics of the human spliceosomal proteome

Korneta I, Magnus M, 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

Rational engineering of sequence specificity in R.MwoI restriction endonuclease

Skowronek K, Boniecki MJ, Kluge B, Bujnicki JM

Nucleic Acids Res. 2012

MetaLocGramN: A meta-predictor of protein subcellular localization for Gram-negative bacteria

Magnus M, Pawlowski M, Bujnicki JM

Biochim Biophys Acta. 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

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

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

Intrinsic disorder in the human spliceosomal proteome

Korneta I, Bujnicki JM

PLoS Comput Biol. 2012

Molecular evolution of dihydrouridine synthases

Kasprzak JM, Czerwoniec A, Bujnicki JM

BMC Bioinformatics. 2012

MetaDisorder: A meta-server for the prediction of intrinsic disorder in proteins

Kozlowski LP, Bujnicki JM

BMC Bioinformatics. 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

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

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

"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

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

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

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

Rother K, Rother M, Boniecki M, Puton T, Bujnicki JM

Rother K, Rother M, Boniecki M, Puton T, Bujnicki JM

J Mol Model.. 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

DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking

Tuszynska I, Bujnicki JM

BMC Bioinformatics. 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

ModeRNA: a tool for comparative modeling of RNA 3D structure

Rother M, Rother K, Puton T, Bujnicki JM

Nucleic Acids Res. 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

Identification and modeling of a phosphatase-like domain in a tRNA 2'-O-ribosyl phosphate transferase Rit1p

Czerwoniec A, Bujnicki JM

Cell Cycle. 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

Databases and bioinformatics tools for the study of DNA repair

Milanowska K, Rother K, Bujnicki JM

Mol Biol Int. 2011

RNA tertiary structure prediction with ModeRNA

Rother M, Rother K, Puton T, Bujnicki JM

Brief Bioinform. 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

Virtual screening strategies in drug design - methods and applications

Bielska E, Lucas X, Czerwoniec A, Kasprzak JM, Kaminska KH, Bujnicki JM

BioTechnologia. 2011

FILTREST3D: discrimination of structural models using restraints from experimental data.

Gajda MJ, Tuszynska I, Kaczor M, Bakulina AY, Bujnicki JM

Bioinformatics. 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

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

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

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

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

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

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 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Modeling of Escherichia coli Endonuclease V structure in complex with DNA.

Majorek KA, Bujnicki JM

J Mol Model. 2009

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

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

YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962

Purta E, O\'Connor M, Bujnicki JM, Douthwaite S

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

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

MetaMQAP: a meta-server for the quality assessment of protein models.

Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM

BMC Bioinformatics. 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

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

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

Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.

Orlowski J, Bujnicki JM

Nucleic Acids Res. 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

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

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

EXOG, a novel paralog of Endonuclease G in higher eukaryotes.

Cymerman IA, Chung I, Beckmann BM, Bujnicki JM, Meiss G

Nucleic Acids Res. 2008

Is AID a monomer in solution?

Bhagwat AS, Carpenter MA, Bujnicki JM

DNA Repair (Amst). 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

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

Bacteriophage Mu Mom protein responsible for DNA modification is a new member of the acyltransferase superfamily.

Kaminska KH, Bujnicki JM

Cell Cycle. 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

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

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

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

Phylogenetic analysis of haloalkane dehalogenases.

Chovancová E, Kosinski J, Bujnicki JM, Damborský J

Proteins. 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

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

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

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

[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

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

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

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

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

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

PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure.

Pietal MJ, Tuszynska I, Bujnicki JM

Bioinformatics. 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

SURF'S UP! - protein classification by surface comparisons

Sasin JM, Godzik A, Bujnicki JM

J Biosci. 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

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

Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.

Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM

BMC Bioinformatics. 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

MODOMICS: a database of RNA modification pathways.

Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM

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

Protein-structure prediction by recombination of fragments.

Bujnicki JM

Chembiochem. 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

Malaria: therapy, genes and vaccines.

Chiang PK, Bujnicki JM, Su X, Lanar DE

Curr Mol Med. 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

Phylogenomic analysis of the GIY-YIG nuclease superfamily.

Dunin-Horkawicz S, Feder M, Bujnicki JM

BMC Genomics. 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

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

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

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

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

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

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

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

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

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

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

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

Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis.

Tkaczuk KL, Obarska A, Bujnicki JM

BMC Evol Biol. 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

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

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

Protein structure prediction: Boltzmann and Darwin (in Polish)

Bujnicki J.M.

Kosmos. 2005

A homology model of restriction endonuclease SfiI in complex with DNA

Chmiel AA, Bujnicki JM, Skowronek KJ

BMC Struct Biol. 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

DNase II is a member of the phospholipase D superfamily.

Cymerman IA, Meiss G, Bujnicki JM

Bioinformatics. 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

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

Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.

Koliński A, Bujnicki JM

Proteins. 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

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

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

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

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

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

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

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

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

Molecular modeling of a psychrophilic β-galactosidase

Tkaczuk KL, Bujnicki JM, Bialkowska A, Bielecki S, Turkiewicz M, Cieslinski H, Kur J

Biocatal Biotransform. 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

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

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

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

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

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

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

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

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

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

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

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

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

COLORADO3D, a web server for the visual analysis of protein structures.

Sasin JM, Bujnicki JM

Nucleic Acids Res. 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

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

Crystallographic and bioinformatic studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology

Bujnicki JM

Curr Protein Pept Sci. 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

Structure, evolution, and inhibitor interaction of S-adenosyl-L-homocysteine hydrolase from Plasmodium falciparum.

Bujnicki JM, Prigge ST, Caridha D, Chiang PK

Proteins. 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

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

Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases

Feder M, Pas J, Wyrwicz LS, Bujnicki JM

Gene. 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

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

Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB.

Kurowski MA, Bhagwat AS, Papaj G, Bujnicki JM

BMC Genomics. 2003

GeneSilico protein structure prediction meta-server.

Kurowski MA, Bujnicki JM

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

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

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

Sequence-structure-function relationships of Tgs1, the yeast snRNA/snoRNA cap hypermethylase

Mouaikel J, Bujnicki JM, Tazi J, Bordonné R

Nucleic Acids Res. 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

STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification.

Sasin JM, Kurowski MA, Bujnicki JM

Bioinformatics. 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

Sequence permutations in the molecular evolution of DNA methyltransferases

Bujnicki JM

BMC Evol Biol. 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

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

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

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

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

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

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

Fold-recognition detects an error in the Protein Data Bank

Bujnicki J, Rychlewski L, Fischer D

Bioinformatics. 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

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

MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase

Pintard L, Bujnicki JM, Lapeyre B, Bonnerot C

EMBO J. 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

Streptococcal Scl1 and Scl2 proteins form collagen-like triple helices.

Xu Y, Keene DR, Bujnicki JM, Höök M, Lukomski S

J Biol Chem. 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

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

Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons.

Bujnicki JM

Acta Biochim Pol. 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

Structure prediction meta server

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

Bioinformatics. 2001

LiveBench-1: continuous benchmarking of protein structure prediction servers

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

Protein Sci. 2001

LiveBench-2: large-scale automated evaluation of protein structure prediction servers.

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

Proteins. 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

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

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 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

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

Sequence analysis and structure prediction of aminoglycoside-resistance 16S rRNA:m7G methyltransferases

Bujnicki JM, Rychlewski L

Acta Microbiol Pol. 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

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

Reassignment of specificities of two cap methyltransferase domains in the reovirus lambda 2 protein

Bujnicki JM, Rychlewski L

Genome Biol. 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

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

Pcons: a neural-network-based consensus predictor that improves fold recognition

Lundström J, Rychlewski L, Bujnicki J, Elofsson A

Protein Sci. 2001

Cloning of enterohemorrhagic Escherichia coli phage VT-2 dam methyltransferase

Radlinska M, Bujnicki JM

Acta Microbiol Pol. 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

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.

Bujnicki JM

FASEB J. 2000

Sequence, structural, and evolutionary analysis of prokaryotic ribosomal protein L11 methyltransferases.

Bujnicki JM

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

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

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