Publikacje

Stefaniak F, Bujnicki JM.

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

PLoS Comput Biol.

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.

RNA and DNA G-quadruplexes bind to human dicer and inhibit its activity.

Cell Mol Life Sci.

Ponce-Salvatierra A, Boccaletto P, Bujnicki JM.

DNAmoreDB, a database of DNAzymes.

Nucleic Acids Res.

Wirecki TK, Merdas K, Bernat A, Boniecki MJ, Bujnicki JM, Stefaniak F.

RNAProbe: a web server for normalization and analysis of RNA structure probing data.

Nucleic Acids Res.

Miao Z et al. (Boniecki MJ, Bujnicki JM, Joshi A, Magnus M, Piatkowski P, Pluta R.)

RNA-Puzzles Round IV: 3D Structure Predictions of Four Ribozymes and Two Aptamers.

RNA

Lambert AR, Hallinan JP, Werther R, Głów D, Stoddard BL.

Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition.

Structure

Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM, Westhof E, Szachniuk M, Miao Z.

RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.

Nucleic Acids Res.

Jaciuk M, Swuec P, Gaur V, Kasprzak JM, Renault L, Dobrychłop M, Nirwal S, Bujnicki JM, Costa A, Nowotny M.

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.

DNA Repair (Amst).

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.

Development of Dual Chitinase Inhibitors as Potential New Treatment for Respiratory System Diseases.

J Med Chem.

Sulej AA

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

BMC Res Notes.

Nowacka M, Boccaletto P, Jankowska E, Jarzynka T, Bujnicki JM, Dunin-Horkawicz S.

RRMdb – an evolutionary-oriented database of RNA recognition motif sequences.

Database

de Crecy-Lagard V, Boccaletto P, Mangleburg C, Sharma P, Lowe T, Leidel S, Bujnicki JM.

Matching tRNA modifications in humans to their known and predicted enzymes.

Nucleic Acids Res.

Stasiewicz J, Mukherjee S, Nithin C, Bujnicki JM.

QRNAS: software tool for refinement of nucleic acid structures.

BMC Struct Biol.

The RNAcentral Consortium (Bujnicki JM, Boccaletto P)

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

Nucleic Acids Res.

Radom M, Machnicka MA, Krwawicz J, Bujnicki JM, Formanowicz P

Petri net-based model of the human DNA base excision repair pathway.

PLoS One

Magnus M, Kappel K, Das R, Bujnicki JM

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

BMC Bioinformatics

Nowacka M, Fernandes H, Kiliszek A, Bernat A, Lach G, Bujnicki JM.

Specific interaction of zinc finger protein Com with RNA and the crystal structure of a self-complementary RNA duplex recognized by Com.

PLoS One

Czapinska H, Siwek W, Szczepanowski RH, Bujnicki JM, Bochtler M, Skowronek KJ.

Crystal Structure and Directed Evolution of Specificity of NlaIV Restriction Endonuclease.

J Mol Biol.

Mitkowski P, Jagielska E, Nowak E, Bujnicki JM, Stefaniak F, Niedziałek D, Bochtler M, Sabała I.

Structural bases of peptidoglycan recognition by lysostaphin SH3b domain.

Sci Rep.

Ponce-Salvatierra A, Astha, Merdas K, Chandran N, Ghosh P, Mukherjee S, Bujnicki JM.

Computational modeling of RNA 3D structure based on experimental data.

Biosci Rep.

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.

Discovery of selective, orally bioavailable inhibitor of mouse chitotriosidase.

28(3)

Voigt C, Dobrychlop M, Kruse E, Czerwoniec A, Kasprzak JM, Bytner P, Campo CD, Leeder WM, Bujnicki JM, Göringer HU.

The OB-fold proteins of the Trypanosoma brucei editosome execute RNA-chaperone activity.

Nucleic Acids Res.

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

Positioning Europe for the EPITRANSCRIPTOMICS challenge.

RNA Biol.

Toczydlowska-Socha D, Zielinska MM, Kurkowska M, Astha, Almeida CF, Stefaniak F, Purta E, Bujnicki JM.

Human RNA cap1 methyltransferase CMTr1 cooperates with RNA helicase DHX15 to modify RNAs with highly structured 5' termini.

Philos Trans R Soc Lond B Biol Sci.

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

Crystal structure of human Acinus RNA recognition motif domain.

PeerJ.

Nithin C, Ghosh P, Bujnicki JM.

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

Genes (Basel)

Kumari P, Aeschimann F, Gaidatzis D, Keusch JJ, Ghosh P, Neagu A, Pachulska-Wieczorek K, Bujnicki JM, Gut H, Großhans H, Ciosk R.

Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition.

Nat Commun.

Foik IP, Tuszynska I, Feder M, Purta E, Stefaniak F, Bujnicki JM.

Novel inhibitors of the rRNA ErmC' methyltransferase to block resistance to macrolides, lincosamides, streptogramine B antibiotics.

Eur J Med Chem.

Pluta R, Espinosa M.

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

Wiley Interdiscip Rev RNA

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.

MODOMICS: a database of RNA modification pathways. 2017 update.

Nucleic Acids Res.

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.

RNArchitecture: a database and a classification system of RNA families, with a focus on structural information.

Nucleic Acids Res.

Dzananovic E, Astha, Chojnowski G, Deo S, Booy EP, Padilla-Meier P, McEleney K, Bujnicki JM, Patel TR, McKenna SA.

Impact of the structural integrity of the three-way junction of adenovirus VAI RNA on PKR inhibition.

PLoS One

Chawla M, Chermak E, Zhang Q, Bujnicki JM, Oliva R, Cavallo L.

Occurrence and stability of lone pair-π stacking interactions between ribose and nucleobases in functional RNAs.

Nucleic Acids Res.

Piątkowski P, Jabłońska J, Żyła A, Niedziałek, Matelska D, Jankowska E, Waleń T, Dawson WK, Bujnicki JM.

SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments.

Nucleic Acids Res.

Budzko L, Jackowiak P, Kamel K, Sarzynska J, Bujnicki JM, Figlerowicz M

Mutations in human AID differentially affect its ability to deaminate cytidine and 5-methylcytidine in ssDNA substrates in vitro

Sci Rep

Karlowicz A, Wegrzyn K, Gross M, Kaczynska D, Ropelewska M, Siemiątkowska M, Bujnicki JM, Konieczny I

Defining the crucial domain and amino acid residues in bacterial Lon protease for DNA binding and processing of DNA-interacting substrates

J Biol Chem

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-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

RNA

Patel T, Chojnowski G, Astha, Koul A, McKenna S, Bujnicki JM

Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering and computational methods

Methods

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

Sequence-specific endoribonucleases.

Postępy Biochemii

Dawson WK, Maciejczyk M, Jankowska EJ, Bujnicki JM

Coarse-grained modeling of RNA 3D structure

Methods

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

tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs

Methods

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

Asymmetric DNA methylation by dimeric EcoP15I DNA methyltransferase

Biochimie

Pawlowski M, Kozlowski L, Kloczkowski A

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

Proteins

Iskierko Z, Sharma PS, Prochowicz D, Fronc K, D'Souza F, Toczydłowska D, Stefaniak F, Noworyta K

Molecularly Imprinted Polymer (MIP) Film with Improved Surface Area Developed by Using Metal-Organic Framework (MOF) for Sensitive Lipocalin (NGAL) Determination.

ACS Appl Mater Interfaces.

Glow D, Kurkowska M, Czarnecka J, Szczepaniak K, Pianka D, Kappert V, Bujnicki JM, Skowronek KJ

Identification of protein structural elements responsible for the diversity of sequence preferences among Mini-III RNases.

Sci Rep.

Van Laer B, Roovers M, Wauters L, Kasprzak JM, Dyzma M, Deyaert E, Singh R, Feller A, Bujnicki JM, Droogmans L, Versées W

Structural and functional insights into tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue

Nucleic Acids Res

Dawson WK, Bujnicki JM

Computational modeling of RNA 3D structures and interactions

Curr Opin Struct Biol

Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction

Nucleic Acids Res

Ukleja M, Cuellar J, Siwaszek A, Kasprzak JM, Czarnocki-Cieciura M, Bujnicki JM, Dziembowski A, Valpuesta J

The architecture of the Schizosaccharomyces pombe CCR4-NOT complex

Nature Commun

Matelska D, Kurkowska M, Purta E, Bujnicki JM, Dunin-Horkawicz S

Loss of conserved non-coding RNAs in genomes of bacterial endosymbionts

Genome Biol Evol

Yahara K, Furuta Y, Morimoto S, Kikutake C, Komukai S, Matelska D, Dunin-Horkawicz S, Bujnicki JM, Uchiyama I, Kobayashi I

Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori

DNA Res

Magnus MM, Boniecki MJ, Dawson WK, Bujnicki JM

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

Nucleic Acids Res.

Machnicka AM, Kaminska KH, Dunin-Horkawicz S, Bujnicki JM.

Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes.

BMC Bioinformatics

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

RNAcentral: a comprehensive database of non-coding RNA sequences

Nucleic Acids Res

Zheng H, Shabalin I, Handing K, Bujnicki JM, Minor M

Magnesium binding architectures in RNA crystal structures: validation binding preferences, classification, and motif detection

Nucleic Acids Res

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

NPDock – a web server for protein-nucleic acid docking

Nucleic Acids Res

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

Biochemical Characterization and Validation of a Catalytic Site of a Highly Thermostable Ts2631 Endolysin from the Thermus scotoductus Phage vB_Tsc2631

PLoS One

Philips A, Lach G, Bujnicki JM

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

Methods Enzymol

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-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

RNA

Liu S, Mozaffari-Jovin S, Wollenhaupt J, Santos KF, Theuser M, Dunin-Horkawicz S, Fabrizio P, Bujnicki JM, Lührmann R, Wahl MC

A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing

eLife

Glow D, Pianka D, Sulej A, Kozlowski L, Czarnecka J, Chojnowski G, Skowronek KJ, Bujnicki JM

Sequence-specific cleavage of dsRNA by Mini-III RNase

Nucleic Acids Res

Deo S, Patel TR, Chojnowski G, Koul A, Dzananovic E, McEleney K, Bujnicki JM, McKenna SA

Characterization of the termini of the West Nile virus genome and their interactions with the small isoform of the 2' 5'-Oligoadenylate Synthetase family

J Struct Biol

Czerwoniec A, Kasprzak JM, Bytner P, Dobrychlop M, Bujnicki JM

Structure and intrinsic disorder of the proteins of the Trypanosoma brucei editosome

FEBS Lett

Chojnowski G, Walen T, Piatkowski P, Potrzebowski W, Bujnicki JM

Brickworx builds recurrent RNA and DNA structural motifs into medium and low-resolution electron density maps

Acta Crystallogr D Biol Crystallogr

Chawla M, Oliva R, Bujnicki JM, Cavallo L

An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies

Nucleic Acids Res

Boekema C, Owens F, Love A, Li Z, Sakkaris P, Dawson WK

A magnetic origin of cuprate superconductivity? A MaxEnt-mu SR view

Int J Mod Phys B

Blatter M, Dunin-Horkawicz S, Grishina I, Maris C, Thore S, Maier T, Bindereif A, Bujnicki JM, Allain FHT

The signature of the five-stranded vRRM fold defined by functional, structural and computational analysis of the hnRNP L protein

J Mol Biol

Bocian-Ostrzycka KM, Łasica AM, Dunin-Horkawicz S, Grzeszczuk MJ, Drabik K, Dobosz AM, Godlewska R, Nowak E, Collet J-F, Jagusztyn-Krynicka EK

Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain

Frontiers in Microbiology

Roszczenko P, Grzeszczuk M, Kobierecka P, Wywial E, Urbanowicz P, Wincek P, Nowak E, Jagusztyn-Krynicka EK

Helicobacter pylori HP0377, a member of the Dsb family, is an untypical multifunctional CcmG that cooperates with dimeric thioldisulfide oxidase HP0231

BMC Microbiol.

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

Distribution and frequencies of post-transcriptional modifications in tRNAs.

RNA Biol.

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

RNA methyltransferases involved in 5' cap biosynthesis.

RNA Biol.

Szczepaniak K, Lach G, Bujnicki JM, Dunin-Horkawicz S

Designability landscape reveals sequence features that define axial helix rotation in four-helical homo-oligomeric antiparallel coiled-coil structures

J Struct Biol.

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

Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA

PLoS One.

Walen T, Chojnowski G, Gierski P,Bujnicki JM,

ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes

Nucleic Acids Res.

Ramos-Molina B, Lambertos A, Lopez-Contreras AJ, Kasprzak JM, Czerwoniec A, Bujnicki JM, Cremades A, Penafiel R

Structural and degradative aspects of ornithine decarboxylase antizyme inhibitor 2

FEBS Open Bio.

Sierocka I, Kozlowski LP, Bujnicki JM, Jarmolowski A, Szweykowska-Kulinska Z

Female-specific gene expression in dioecious liverwort Pellia endiviifolia is developmentally regulated and connected to archegonia production

BMC Plant Biol.

Magnus M, Matelska D, Lach G, Chojnowski G, Boniecki MJ, Purta E, Dawson W, Dunin-Horkawicz S, Bujnicki JM

Computational modeling of RNA 3D structures, with the aid of experimental restraints

RNA Biol.

Rother K, Rother M, Skiba P, Bujnicki JM

Automated modeling of RNA 3D structure

Methods Mol Biol

Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler M

Structural basis of the methylation specificity of R.DpnI

Nucleic Acids Res.

Majorek KA, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A, Nowotny M, Ginalski K, Bujnicki JM

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification

Nucleic Acids Res.

Toczyłowska-Mamińska R, Olszewska A, Laskowski M, Bednarczyk P, Skowronek K, Szewczyk A

Potassium channel in the mitochondria of human keratinocytes

J Invest Dermatol

Sadowski Ł, Jastrzębski K, Purta E, Hellberg C, Miaczynska M

Labeling of platelet-derived growth factor by reversible biotinylation to visualize its endocytosis by microscopy

Methods Enzymol.

Crochemore M, Iliopoulos CS, Kubica M, Radoszewski J, Rytter W, Stencel K, Walen T

New simple efficient algorithms computing powers and runs in strings

Discrete Applied Mathematics

Smietanski M, Werner M, Purta E, Kaminska KH, Stepinski J, Darzynkiewicz E, Nowotny M, Bujnicki JM

Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation

Nat Commun

Chojnowski G, Walen T, Bujnicki JM

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

Nucleic Acids Res.

Dzananovic E, Patel TR, Chojnowski G, Boniecki MJ, Deo S, McEleney K, Harding SE, Bujnicki JM, McKenna SA

Solution conformation of Adenovirus Virus Associated RNA-I and its interaction with PKR

J Struct Biol

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

Novel Highly Thermostable Endolysin from Thermus scotoductus MAT2119 Bacteriophage Ph2119 with Amino Acid Sequence Similarity to Eukaryotic Peptidoglycan Recognition Proteins

Appl Environ Microbiol

Tuszynska I, Matelska D, Magnus M, Chojnowski G, Kasprzak JM, Kozlowski LP, Dunin-Horkawicz S, Bujnicki JM

Computational modeling of protein-RNA complex structures

Methods

Xu C, Liu R, Mehta AK, Guerrero-Ferreira RC, Wright ER, Dunin-Horkawicz S, Morris K, Serpell LC, Zuo X, Wall JS, Conticello VP

Rational design of helical nanotubes from self-assembly of coiled-coil lock washers

J Am Chem Soc.

Philips A, Milanowska K, Lach G, Bujnicki JM

LigandRNA: computational predictor of RNA-ligand interactions

RNA

Czeredys M, Samluk L, Michalec K, Tułodziecka K, Skowronek K, Nałęcz KA

Caveolin-1 - a novel interacting partner of organic cation/carnitine transporter (octn2): effect of protein kinase C on this interaction in rat astrocytes.

PLoS One

Matelska D, Purta E, Panek S, Boniecki MJ, Bujnicki JM, Dunin-Horkawicz S

S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA

RNA

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

A linear time algorithm for consecutive permutation pattern matching

Information Processing Letters

Bednarczyk P, Wieckowski MR, Broszkiewicz M, Skowronek K, Siemen D, Szewczyk A

Putative Structural and Functional Coupling of the Mitochondrial BKCa Channel to the Respiratory Chain

PLoS One

Crochemore M, Iliopoulos C.S, Kociumaka T, Kubica M, Pachocki J, Radoszewski J, Rytter W,Tyczyński W, Waleń T

A note on efficient computation of all Abelian periods in a string

Information Processing Letters

Pawlowski M, Bogdanowicz A, Bujnicki JM

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

Nucleic Acids Res

Lukasiak P, Antczak M, Ratajczak T, Bujnicki JM, Szachniuk M, Adamiak RW, Popenda M, Blazewicz J

RNAlyzer--novel approach for quality analysis of RNA structural models

Nucleic Acids Res

Bujnicki JM, Tiuryn J

Bioinformatics and computational biology in Poland

PLoS Comput Biol

Puton T, Kozlowski LP, Rother KM, Bujnicki JM

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

Nucleic Acids Res.

Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M

Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid

Nucleic Acids Res

Milanowska K, Mikolajczak K, Lukasik A, Skorupski M, Balcer Z, Machnicka MA, Nowacka M, Rother KM, Bujnicki JM

RNApathwaysDB – a database of RNA maturation and decay pathways

Nucleic Acids Res

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

MODOMICS: a database of RNA modification pathways: 2013 update

Nucleic Acids Res

Kozlowski L, Orlowski J, Bujnicki JM

Structure prediction of alternatively spliced proteins In „Alternative pre-mRNA Splicing: Theory and Protocols: The Complete Guide for Biomedical Scientists”

Rother K, Rother M, Boniecki M, Puton T, Tomala K, Lukasz P, Bujnicki JM

Template-based and template-free modeling of RNA 3D structure: inspirations from protein structure modeling In "RNA Structure Prediction and Modelling"

Kozlowski LP, Bujnicki JM

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

BMC Bioinformatics

Kasprzak JM, Czerwoniec A, Bujnicki JM

Molecular evolution of dihydrouridine synthases

BMC Bioinformatics

Korneta I, Bujnicki JM

Intrinsic disorder in the human spliceosomal proteome

PLoS Comput Biol

Kusio-Kobialka M, Wolanin K, Podszywalow-Bartnicka P, Sikora E, Skowronek K, McKenna SL, Ghizzoni M, Dekker FJ, Piwocka K

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

Apoptosis

Roszczenko P, Radomska KA, Wywial E, Collet JF, Jagusztyn-Krynicka EK

A novel insight into the oxidoreductase activity of Helicobacter pylori HP0231 protein

PLoS One

Al-Haggar M, Madej-Pilarczyk A, Kozlowski L, Bujnicki JM, Yahia S, Abdel-Hadi D, Shams A, Ahmad N, Hamed S, Puzianowska-Kuznicka M

A novel homozygous p.Arg527Leu LMNA mutation in two unrelated egyptian families causes overlapping mandibuloacral dysplasia and progeria syndrome

Eur J Hum Genet

Magnus M, Pawlowski M, Bujnicki JM

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

Biochim Biophys Acta

Skowronek K, Boniecki MJ, Kluge B, Bujnicki JM

Rational engineering of sequence specificity in R.MwoI restriction endonuclease

Nucleic Acids Res

Poleszak K, Kaminska KH, Dunin-Horkawicz S, Lupas A, Skowronek KJ, Bujnicki JM

Delineation of structural domains and identification of functionally important residues in DNA repair enzyme Exonuclease VII

Nucleic Acids Res

Korneta I, Magnus M, Bujnicki JM

Structural bioinformatics of the human spliceosomal proteome

Nucleic Acids Res

Drozdz M, Piekarowicz A, Bujnicki JM, Radlinska M

Novel non-specific DNA adenine methyltransferases

Nucleic Acids Res

Sulej AA, Tuszynska I, Skowronek KJ, Nowotny M, Bujnicki JM

Sequence-specific cleavage of the RNA strand in DNA-RNA hybrids by the fusion of ribonuclease H with a zinc finger

Nucleic Acids Res

Pawlowski M, Bujnicki JM

The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement

BMC Bioinformatics

Pietal MJ, Szostak N, Rother KM, Bujnicki JM

RNAmap2D -- calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures

BMC Bioinformatics

Siwek W, Czapinska H, Bochtler M, Bujnicki JM, Skowronek K

Crystal structure and mechanism of action of the N6-methyladenine dependent type IIM restriction endonuclease

Nucleic Acids Res

Samluk L, Czeredys M, Skowronek K, Nałęcz KA

Protein kinase C regulates amino acid transporter ATB

Biochem Biophys Res Commun.

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

Statins Impair Glucose Uptake in Tumor Cells

Neoplasia

Lach G, DeKievet M, Jentschura UD

Einstein–Hopf drag, Doppler shift of thermal radiation and blackbody drag: Three perspectives on quantum friction

Cent. Eur. J. Phys.

Fislage M, Roovers M, Tuszynska I, Bujnicki JM, Droogmans L, Versées W

Crystal structures of the tRNA:m(2)G6 methyltransferase Trm14/TrmN from two domains of life

Nucleic Acids Res

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-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

RNA

Chojnowski G, Bujnicki JM, Bochtler M

RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes

Bioinformatics

Zylicz-Stachula A, Zolnierkiewicz O, Lubys A, Ramanauskaite D, Mitkaite G, Bujnicki JM, Skowron P

Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities

BMC Mol Biol

Roovers M, Oudjama Y, Fislage M, Bujnicki JM, Versées W, Droogmans L

The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N2-methylguanosine at position 6 in tRNA

RNA

Nakagome S, Mano S, Kozlowski L, Bujnicki JM, Shibata H, Fukumaki Y, Kidd JR, Kidd KK, Kawamura S, Oota H

Crohn's Disease Risk Alleles on the NOD2 Locus Have Been Maintained by Natural Selection on Standing Variation

Mol Biol Evol

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

Computational methods for prediction of protein-RNA interactions

J Struct Biol

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

A toolbox for developing bioinformatics software

Brief Bioinform

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

Structure and operation of the DNA-translocating type I DNA restriction enzymes

Genes Dev

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

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

Bioinformatics

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

Virtual screening strategies in drug design - methods and applications

BioTechnologia

Sikorski K, Czerwoniec A, Bujnicki JM, Wesoly J, Bluyssen HAR

STAT1 as a novel therapeutical target in pro-atherogenic signal integration of IFNg, TLR4 and IL-6 in vascular disease

Cytokine Growth Factor Rev.

Rother M, Rother K, Puton T, Bujnicki JM

RNA tertiary structure prediction with ModeRNA

Brief Bioinform

Milanowska K, Rother K, Bujnicki JM

Databases and bioinformatics tools for the study of DNA repair

Mol Biol Int

Liu J, Ganapathy K, Wywial E, Bujnicki JM, Nwogwugwu CA, Nes WD

Effect of substrate features and mutagenesis of active site tyrosine residues on the reaction course catalysed by Trypanosoma brucei sterol C-24-methyltransferase

Biochem J

Czerwoniec A, Bujnicki JM

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

Cell Cycle

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

RNAcentral: A vision for an international database of RNA sequences

RNA

Rother M, Rother K, Puton T, Bujnicki JM

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

Nucleic Acids Res

Werner M, Purta E, Kaminska KH, Cymerman IA, Campbell DA, Mittra B, Zamudio JR, Sturm NR, Jaworski J, Bujnicki JM

2'-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family

Nucleic Acids Res

Tuszynska I, Bujnicki JM

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

BMC Bioinformatics

Rother M, Milanowska K, Puton T, Jeleniewicz J, Rother K, Bujnicki JM

ModeRNA server: an online tool for modeling RNA 3D structures

Bioinformatics

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

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

J Mol Model.

Spears JL, Rubio MA, Gaston KW, Wywial E, Strikoudis A, Bujnicki JM, Papavasiliou FN, Alfonzo JD

A single zinc ion is sufficient for an active Trypanosoma brucei tRNA editing deaminase

J Biol Chem

Tesfazgi Mebrhatu M, Wywial E, Ghosh A, Michiels CW, Lindner AB, Taddei F, Bujnicki JM, Van Melderen L, Aertsen A

Evidence for an evolutionary antagonism between Mrr and Type III modification systems.

Nucleic Acids Res

Rother K, Rother M, Boniecki M, Puton T, Tomala K, Lukasz P, Bujnicki JM

Template-based and template-free modeling of RNA 3D structure: inspirations from protein structure modeling

RNA Structure Prediction and Modelling

Kozlowski L, Orlowski J, Bujnicki JM

Structure prediction of alternatively spliced proteins

RNA splicing: The complete guide

Husain N, Obranic S, Koscinski L, Seetharaman J, Babic F, Bujnicki JM, Maravic-Vlahovicek G, Sivaraman J

Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit

Nucleic Acids Res

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

"4D Biology for health and disease" workshop report

N Biotechnol

Milanowska K, Krwawicz J, Papaj G, Kosinski J, Poleszak K, Lesiak J, Osinska E, Rother K, Bujnicki JM

REPAIRtoire-a database of DNA repair pathways

Nucleic Acids Res

Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA

BioCatalogue: a universal catalogue of web services for the life sciences

Nucleic Acids Res

Tkaczuk KL

Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site

J Mol Model.

Rother K, Hoffmann S, Bulik S, Hoppe A, Gasteiger J, Holzhütter HG

IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities

Biophys J.

Khan F, Furuta Y, Kawai M, Kaminska KH, Ishikawa K, Bujnicki JM, Kobayashi I

A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI).

Nucleic Acids Res

Tuszynska I, Bujnicki JM

Predicting atomic details of the unfolding pathway for YibK, a knotted protein from the SPOUT superfamily

J Biomol Struct Dyn

Kaminska KH, Purta E, Hansen LH, Bujnicki JM, Vester B, Long KS

Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria.

Nucleic Acids Res

Zhou X, Chua TK, Tkaczuk KL, Bujnicki JM, Sivaraman J

The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket.

J Struct Biol

Pukáncsik M, Békési A, Klement E, Hunyadi-Gulyás E, Medzihradszky KF, Kosinski J, Bujnicki JM, Alfonso C, Rivas G, Vértessy BG

Physiological truncation and domain organization of a novel uracil-DNA-degrading factor.

FEBS J

Zhang Z, Theler D, Kaminska KH, Hiller M, de la Grange P, Pudimat R, Rafalska I, Heinrich B, Bujnicki JM, Allain FH, Stamm S

The YTH domain is a novel RNA binding domain.

J Biol Chem

Pukszta S, Schilke B, Dutkiewicz R, Kominek J, Moczulska K, Stepien B, Reitenga KG, Bujnicki JM, Williams B, Craig EA, Marszalek J

Co-evolution-driven switch of J-protein specificity towards an Hsp70 partner.

EMBO Rep

Kempenaers M, Roovers M, Oudjama Y, Tkaczuk KL, Bujnicki JM, Droogmans L

New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA.

Nucleic Acids Res

Husain N, Tkaczuk KL, Tulsidas SR, Kaminska KH, Cubrilo S, Maravić-Vlahovicek G, Bujnicki JM, Sivaraman J

Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m7G methyltransferases.

Nucleic Acids Res

Kosinski J, Hinrichsen I, Bujnicki JM, Friedhoff P, Plotz G

Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair.

Hum Mutat

Chua TK, Seetharaman J, Kasprzak JM, Ng C, Patel BK, Love C, Bujnicki JM, Sivaraman J

Crystal structure of a fructokinase homolog from Halothermothrix orenii

J Struct Biol

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

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

Bioinformatics

Majorek KA, Bujnicki JM

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

J Mol Model

Fink G, Hajdo L, Skowronek KJ, Reuther C, Kasprzak AA, Diez S

The mitotic kinesin-14 Ncd drives directional microtubule-microtubule sliding.

Nat Cell Biol

Czerwoniec A, Dunin-Horkawicz S, Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Grosjean H, Rother K

MODOMICS: a database of RNA modification pathways. 2008 update

Nucleic Acids Res

Nakonieczna J, Kaczorowski T, Obarska-Kosinska A, Bujnicki JM

Functional analysis of MmeI from methanol utilizer Methylophilus methylotrophus, a subtype IIC restriction-modification enzyme related to type I enzymes.

Appl Environ Microbiol

Kennaway CK, Obarska-Kosinska A, White JH, Tuszynska I, Cooper LP, Bujnicki JM, Trinick J, Dryden DT

The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein

Nucleic Acids Res

Pierechod M, Nowak A, Saari A, Purta E, Bujnicki JM, Konieczny I

Conformation of a plasmid replication initiator protein affects its proteolysis by ClpXP system

Protein Sci

Matsumoto Y, Oota H, Asaoka Y, Nishina H, Watanabe K, Bujnicki JM, Oda S, Kawamura S, Mitani H

Medaka: a promising model animal for comparative population genomics.

BMC Res Notes

Bauer RA, Rother K, Moor P, Reinert K, Steinke T, Bujnicki JM

Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors

Algorithms

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

YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA.

Mol Microbiol

Pawłowski M, Lasica AM, Jagusztyn-Krynicka EK, Bujnicki JM

AAN82231 protein from uropathogenic E. coli CFT073 is a close paralog of DsbB enzymes and does not belong to the DsbI family

Pol J Microbiol

Zylicz-Stachula A, Bujnicki JM, Skowron PM

Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family.

BMC Mol Biol

Palfi Z, Jaé N, Preusser C, Kaminska KH, Bujnicki JM, Lee JH, Günzl A, Kambach C, Urlaub H, Bindereif A

SMN-assisted assembly of snRNP-specific Sm cores in trypanosomes.

Genes Dev

Pena V, Jovin SM, Fabrizio P, Orlowski J, Bujnicki JM, Lührmann R, Wahl MC

Common design principles in the spliceosomal RNA helicase Brr2 and in the Hel308 DNA helicase.

Mol Cell

Kolmos E, Nowak M, Werner M, Fischer K, Schwarz G, Mathews S, Schoof H, Nagy F, Bujnicki JM, Davis SJ

Integrating ELF4 into the circadian system through combined structural and functional studies.

HFSP J

Leski TA, Caswell CC, Pawlowski M, Klinke DJ, Bujnicki JM, Hart SJ, Lukomski S

Identification and classification of bcl genes and proteins of Bacillus cereus group organisms and their application in Bacillus anthracis detection and fingerprinting.

Appl Environ Microbiol

Maravić Vlahovicek G, Cubrilo S, Tkaczuk KL, Bujnicki JM

Modeling and experimental analyses reveal a two-domain structure and amino acids important for the activity of aminoglycoside resistance methyltransferase Sgm.

Biochim Biophys Acta

Vasu K, Saravanan M, Bujnicki JM, Nagaraja V

Structural integrity of the beta beta alpha-Metal finger motif is required for DNA binding and stable protein-DNA complex formation in R.KpnI.

Biochim Biophys Acta

Kaminska KH, Baraniak U, Boniecki M, Nowaczyk K, Czerwoniec A, Bujnicki JM

Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms(2)io(6)A37 in tRNA.

Proteins

Roovers M, Oudjama Y, Kaminska KH, Purta E, Caillet J, Droogmans L, Bujnicki JM

Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA.

Proteins

Kaminska KH, Bujnicki JM

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

Cell Cycle

Mittra B, Zamudio JR, Bujnicki JM, Stepinski J, Darzynkiewicz E, Campbell DA, Sturm NR

The TbMTr1 spliced leader RNA cap 1 2'-O-ribose methyltransferase from Trypanosoma brucei acts with substrate specificity

J Biol Chem

Feder M, Purta E, Koscinski L, Cubrilo S, Maravic Vlahovicek G, Bujnicki JM

Virtual screening and experimental verification to identify potential inhibitors of the ErmC methyltransferase responsible for bacterial resistance against macrolide antibiotics.

ChemMedChem

Bhagwat AS, Carpenter MA, Bujnicki JM

Is AID a monomer in solution?

DNA Repair (Amst)

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

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

Nucleic Acids Res

Sen TZ, Kloster M, Jernigan RL, Kolinski A, Bujnicki JM, Kloczkowski A

Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA.

Biophys J

Chua TK, Bujnicki JM, Tan TC, Huynh F, Patel BK, Sivaraman J

The structure of sucrose phosphate synthase from Halothermothrix orenii reveals its mechanism of action and binding mode.

Plant Cell

Roovers M, Kaminska KH, Tkaczuk KL, Gigot D, Droogmans L, Bujnicki JM

The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK).

Nucleic Acids Res

Orlowski J, Bujnicki JM

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

Nucleic Acids Res

White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM, Johnson AW

Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits.

Mol Cell Biol

Kosinski J, Plotz G, Guarné A, Bujnicki JM, Friedhoff P

The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family.

J Mol Biol

Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Douthwaite S

YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA.

RNA

Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM

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

BMC Bioinformatics

Sunita S, Tkaczuk KL, Purta E, Kasprzak JM, Douthwaite S, Bujnicki JM, Sivaraman J

Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes.

J Mol Biol

Obarska-Kosinska A, Taylor JE, Callow P, Orlowski J, Bujnicki JM, Kneale GG

HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling.

J Mol Biol

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

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

J Mol Biol

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

IAPs contain an evolutionarily conserved ubiquitin-binding domain that regulates NF-kappaB as well as cell survival and oncogenesis.

Nat Cell Biol

Orlowski J, Mebrhatu MT, Michiels CW, Bujnicki JM, Aertsen A

Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr.

Biochem Biophys Res Commun

Zamudio JR, Mittra B, Foldynová-Trantírková S, Zeiner GM, Lukes J, Bujnicki JM, Sturm NR, Campbell DA

The 2'-O-ribose methyltransferase for cap 1 of spliced leader RNA and U1 small nuclear RNA in Trypanosoma brucei

Mol Cell Biol

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

Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.

BMC Bioinformatics

Sunita S, Purta E, Durawa M, Tkaczuk KL, Swaathi J, Bujnicki JM, Sivaraman J

Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC.

Nucleic Acids Res

Schäfer P, Cymerman IA, Bujnicki JM, Meiss G

Human lysosomal DNase IIalpha contains two requisite PLD-signature (HxK) motifs: evidence for a pseudodimeric structure of the active enzyme species.

Protein Sci

Sasin JM, Godzik A, Bujnicki JM

SURF'S UP! - protein classification by surface comparisons

J Biosci

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

Transcriptome profile of human colorectal adenomas.

Mol Cancer Res

Pietal MJ, Tuszynska I, Bujnicki JM

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

Bioinformatics

Pena V, Liu S, Bujnicki JM, Lührmann R, Wahl MC

Structure of a multipartite protein-protein interaction domain in splicing factor prp8 and its link to retinitis pigmentosa.

Mol Cell

Ozanick SG, Bujnicki JM, Sem DS, Anderson JT

Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding.

Nucleic Acids Res

Orlowski J, Boniecki M, Bujnicki JM

I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition

Bioinformatics

Miyazono K, Watanabe M, Kosinski J, Ishikawa K, Kamo M, Sawasaki T, Nagata K, Bujnicki JM, Endo Y, Tanokura M, Kobayashi I

Novel protein fold discovered in the PabI family of restriction enzymes.

Nucleic Acids Res

Liu Y, Li Z, Lin Q, Kosinski J, Seetharaman J, Bujnicki JM, Sivaraman J, Hew CL

Structure and evolutionary origin of Ca(2+)-dependent herring type II antifreeze protein.

PLoS One

Kudan EV, Brevnov MG, Subach OM, Rechkoblit OA, Buĭnitskiĭ IaM, Gromova ES

[Probing of contacts between EcoRII DNA methyltransferase and DNA using substrate analogs and molecular modeling].

Mol Biol (Mosk)

Kosinski J, Kubareva E, Bujnicki JM

A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering.

Proteins

Koscinski L, Feder M, Bujnicki JM

Identification of a missing sequence and functionally important residues of 16S rRNA:m(1)A1408 methyltransferase KamB that causes bacterial resistance to aminoglycoside antibiotics.

Cell Cycle

Jakubauskas A, Giedriene J, Bujnicki JM, Janulaitis A

Identification of a single HNH active site in type IIS restriction endonuclease Eco31I

J Mol Biol

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

Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily.

BMC Struct Biol

Chovancová E, Kosinski J, Bujnicki JM, Damborský J

Phylogenetic analysis of haloalkane dehalogenases.

Proteins

Zegers I, Gigot D, van Vliet F, Tricot C, Aymerich S, Bujnicki JM, Kosinski J, Droogmans L

Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase.

Nucleic Acids Res

Zamudio JR, Mittra B, Zeiner GM, Feder M, Bujnicki JM, Sturm NR, Campbell DA

Complete cap 4 formation is not required for viability in Trypanosoma brucei.

Eukaryot Cell

Tkaczuk KL, Obarska A, Bujnicki JM

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

BMC Evol Biol

Skowronek KJ, Kosinski J, Bujnicki JM

Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis.

Proteins

Sikora E, Bielak-Zmijewska A, Magalska A, Piwocka K, Mosieniak G, Kalinowska M, Widlak P, Cymerman IA, Bujnicki JM

Curcumin induces caspase-3-dependent apoptotic pathway but inhibits DNA fragmentation factor 40/caspase-activated DNase endonuclease in human Jurkat cells.

Mol Cancer Ther

Samaranayake M, Bujnicki JM, Carpenter M, Bhagwat AS

Evaluation of molecular models for the affinity maturation of antibodies: roles of cytosine deamination by AID and DNA repair.

Chem Rev

Purta E, van Vliet F, Tkaczuk KL, Dunin-Horkawicz S, Mori H, Droogmans L, Bujnicki JM

The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase.

BMC Mol Biol

Obarska A, Blundell A, Feder M, Vejsadová S, Sisáková E, Weiserová M, Bujnicki JM, Firman K

Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA.

Nucleic Acids Res

Mikula M, Karczmarski J, Dzwonek A, Rubel T, Hennig E, Dadlez M, Bujnicki JM, Bomsztyk K, Ostrowski J

Casein kinases phosphorylate multiple residues spanning the entire hnRNP K length.

Biochim Biophys Acta

Metz J, Wächter A, Schmidt B, Bujnicki JM, Schwappach B

The yeast Arr4p ATPase binds the chloride transporter Gef1p when copper is available in the cytosol.

J Biol Chem

Klimek-Tomczak K, Mikula M, Dzwonek A, Paziewska A, Karczmarski J, Hennig E, Bujnicki JM, Bragoszewski P, Denisenko O, Bomsztyk K, Ostrowski J

Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.

Br J Cancer

Han R, Caswell CC, Lukomska E, Keene DR, Pawlowski M, Bujnicki JM, Kim JK, Lukomski S

Binding of the low-density lipoprotein by streptococcal collagen-like protein Scl1 of Streptococcus pyogenes.

Mol Microbiol

Gros L, Renodon-Cornière A, de Saint Vincent BR, Feder M, Bujnicki JM, Jacquemin-Sablon A

Characterization of prmt7alpha and beta isozymes from Chinese hamster cells sensitive and resistant to topoisomerase II inhibitors.

Biochim Biophys Acta

Godlewska R, Dzwonek A, Mikuła M, Ostrowski J, Pawłowski M, Bujnicki JM, Jagusztyn-Krynicka EK

Helicobacter pylori protein oxidation influences the colonization process.

Int J Med Microbiol

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

THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain.

Nucleic Acids Res

Dunin-Horkawicz S, Feder M, Bujnicki JM

Phylogenomic analysis of the GIY-YIG nuclease superfamily.

BMC Genomics

Cymerman IA, Obarska A, Skowronek KJ, Lubys A, Bujnicki JM

Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease

Proteins

Chiang PK, Bujnicki JM, Su X, Lanar DE

Malaria: therapy, genes and vaccines.

Curr Mol Med

Carpenter M, Divvela P, Pingoud V, Bujnicki J, Bhagwat AS

Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI.

Nucleic Acids Res

Bujnicki JM

Protein-structure prediction by recombination of fragments.

Chembiochem

Bheemanaik S, Bujnicki JM, Nagaraja V, Rao DN

Functional analysis of amino acid residues at the dimerisation interface of KpnI DNA methyltransferase.

Biol Chem

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

MODOMICS: a database of RNA modification pathways.

Nucleic Acids Res

Radlińska M, Piekarowicz A, Galimand M, Bujnicki JM

Cloning and preliminary characterization of a GATC-specific beta2-class DNA:m6A methyltransferase encoded by transposon Tn1549 from Enterococcus spp.

Pol J Microbiol

Radlinska M, Kondrzycka-Dada A, Piekarowicz A, Bujnicki JM

Identification of amino acids important for target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine-scanning mutagenesis of residues at the protein-DNA interface.

Proteins

Raczko AM, Bujnicki JM, Pawlowski M, Godlewska R, Lewandowska M, Jagusztyn-Krynicka EK

Characterization of new DsbB-like thiol-oxidoreductases of Campylobacter jejuni and Helicobacter pylori and classification of the DsbB family based on phylogenomic, structural and functional criteria.

Microbiology

Purushothaman SK, Bujnicki JM, Grosjean H, Lapeyre B

Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA.

Mol Cell Biol

Kosinski J, Steindorf I, Bujnicki JM, Giron-Monzon L, Friedhoff P

Analysis of the quaternary structure of the MutL C-terminal domain.

J Mol Biol

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

FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6.

Proteins

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

Molecular modeling of a psychrophilic β-galactosidase

Biocatal Biotransform

Radlińska M, Piekarowicz A, Galimand M, Bujnicki JM

Cloning and preliminary characterization of a GATC-specific beta2-class DNA:m6A methyltransferase encoded by transposon Tn1549 from Enterococcus spp.

Pol J Microbiol

Radlinska M, Kondrzycka-Dada A, Piekarowicz A, Bujnicki JM

Identification of amino acids important for target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine-scanning mutagenesis of residues at the protein-DNA interface.

Proteins

Raczko AM, Bujnicki JM, Pawlowski M, Godlewska R, Lewandowska M, Jagusztyn-Krynicka EK

Characterization of new DsbB-like thiol-oxidoreductases of Campylobacter jejuni and Helicobacter pylori and classification of the DsbB family based on phylogenomic, structural and functional criteria.

Microbiology

Purta E, van Vliet F, Tricot C, De Bie LG, Feder M, Skowronek K, Droogmans L, Bujnicki JM

Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis.

Proteins

Purushothaman SK, Bujnicki JM, Grosjean H, Lapeyre B

Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA.

Mol Cell Biol

Pingoud V, Sudina A, Geyer H, Bujnicki JM, Lurz R, Lüder G, Morgan R, Kubareva E, Pingoud A

Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences

J Biol Chem

Pingoud V, Geyer H, Geyer R, Kubareva E, Bujnicki JM, Pingoud A

Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII

Mol Biosyst

Pawlak SD, Radlinska M, Chmiel AA, Bujnicki JM, Skowronek KJ

Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII

Nucleic Acids Res

Kosinski J, Steindorf I, Bujnicki JM, Giron-Monzon L, Friedhoff P

Analysis of the quaternary structure of the MutL C-terminal domain.

J Mol Biol

Kosinski J, Feder M, Bujnicki JM

The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function.

BMC Bioinformatics

Koliński A, Bujnicki JM

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

Proteins

Ishikawa K, Watanabe M, Kuroita T, Uchiyama I, Bujnicki JM, Kawakami B, Tanokura M, Kobayashi I

Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi

Nucleic Acids Res

Feder M, Bujnicki JM

Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site.

BMC Genomics

Cymerman IA, Meiss G, Bujnicki JM

DNase II is a member of the phospholipase D superfamily.

Bioinformatics

Chmiel AA, Radlinska M, Pawlak SD, Krowarsch D, Bujnicki JM, Skowronek KJ

A theoretical model of restriction endonuclease NlaIV in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis and circular dichroism spectroscopy.

Protein Eng Des Sel

Chmiel AA, Bujnicki JM, Skowronek KJ

A homology model of restriction endonuclease SfiI in complex with DNA

BMC Struct Biol

Bujnicki J.M.

Protein structure prediction: Boltzmann and Darwin (in Polish)

Kosmos

Armalyte E, Bujnicki JM, Giedriene J, Gasiunas G, Kosiński J, Lubys A

Mva1269I: a monomeric type IIS restriction endonuclease from Micrococcus varians with two EcoRI- and FokI-like catalytic domains.

J Biol Chem

Ye X, O\'Neil PK, Foster AN, Gajda MJ, Kosinski J, Kurowski MA, Bujnicki JM, Friedman AM, Bailey-Kellogg C

Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure.

Protein Sci

Schäfer P, Scholz SR, Gimadutdinow O, Cymerman IA, Bujnicki JM, Ruiz-Carrillo A, Pingoud A, Meiss G

Structural and functional characterization of mitochondrial EndoG, a sugar non-specific nuclease which plays an important role during apoptosis.

J Mol Biol

Sasin JM, Bujnicki JM

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

Nucleic Acids Res

Saravanan M, Bujnicki JM, Cymerman IA, Rao DN, Nagaraja V

Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily.

Nucleic Acids Res

Roovers M, Wouters J, Bujnicki JM, Tricot C, Stalon V, Grosjean H, Droogmans L

A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase

Nucleic Acids Res

Potluri S, Khan AA, Kuzminykh A, Bujnicki JM, Friedman AM, Bailey-Kellogg C

Geometric analysis of cross-linkability for protein fold discrimination.

Pac Symp Biocomput

Paziewska A, Wyrwicz LS, Bujnicki JM, Bomsztyk K, Ostrowski J

Cooperative binding of the hnRNP K three KH domains to mRNA targets.

FEBS Lett

Nes WD, Jayasimha P, Zhou W, Kanagasabai R, Jin C, Jaradat TT, Shaw RW, Bujnicki JM

Sterol methyltransferase: functional analysis of highly conserved residues by site-directed mutagenesis.

Biochemistry

Maravić G, Bujnicki JM, Flögel M

Mutational analysis of basic residues in the N-terminus of the rRNA:m6A methyltransferase ErmC'

Folia Microbiol (Praha)

Koudan EV, Bujnicki JM, Gromova ES

Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy.

J Biomol Struct Dyn

Bujnicki JM, Oudjama Y, Roovers M, Owczarek S, Caillet J, Droogmans L

Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA.

RNA

Bujnicki JM, Feder M, Ayres CL, Redman KL

Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases.

Nucleic Acids Res

Armengaud J, Urbonavicius J, Fernandez B, Chaussinand G, Bujnicki JM, Grosjean H

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.

J Biol Chem

Koudan EV, Bujnicki JM, Gromova ES

Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy.

J Biomol Struct Dyn

Bujnicki JM, Oudjama Y, Roovers M, Owczarek S, Caillet J, Droogmans L

Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA.

RNA

Bujnicki JM, Feder M, Ayres CL, Redman KL

Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases.

Nucleic Acids Res

Armengaud J, Urbonavicius J, Fernandez B, Chaussinand G, Bujnicki JM, Grosjean H

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.

J Biol Chem

Scholz SR, Korn C, Bujnicki JM, Gimadutdinow O, Pingoud A, Meiss G

Experimental evidence for a beta beta alpha-Me-finger nuclease motif to represent the active site of the caspase-activated DNase.

Biochemistry

Sasin JM, Kurowski MA, Bujnicki JM

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

Bioinformatics

Pingoud V, Conzelmann C, Kinzebach S, Sudina A, Metelev V, Kubareva E, Bujnicki JM, Lurz R, Lüder G, Xu SY, Pingoud A

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

J Mol Biol

Mouaikel J, Bujnicki JM, Tazi J, Bordonné R

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

Nucleic Acids Res

Maravić G, Feder M, Pongor S, Flögel M, Bujnicki JM

Mutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC'

J Mol Biol

Maravić G, Bujnicki JM, Feder M, Pongor S, Flögel M

Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions

Nucleic Acids Res

Kurowski MA, Sasin JM, Feder M, Debski J, Bujnicki JM

Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures.

BMC Bioinformatics

Kurowski MA, Bujnicki JM

GeneSilico protein structure prediction meta-server.

Nucleic Acids Res

Kurowski MA, Bhagwat AS, Papaj G, Bujnicki JM

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

BMC Genomics

Kosinski J, Cymerman IA, Feder M, Kurowski MA, Sasin JM, Bujnicki JM

A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation

Proteins

Gordon RK, Ginalski K, Rudnicki WR, Rychlewski L, Pankaskie MC, Bujnicki JM, Chiang PK

Anti-HIV-1 activity of 3-deaza-adenosine analogs. Inhibition of S-adenosylhomocysteine hydrolase and nucleotide congeners.

Eur J Biochem

Feder M, Pas J, Wyrwicz LS, Bujnicki JM

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

Gene

Droogmans L, Roovers M, Bujnicki JM, Tricot C, Hartsch T, Stalon V, Grosjean H

Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures.

Nucleic Acids Res

De Bie LG, Roovers M, Oudjama Y, Wattiez R, Tricot C, Stalon V, Droogmans L, Bujnicki JM

The yggH gene of Escherichia coli encodes a tRNA (m7G46) methyltransferase.

J Bacteriol

Bujnicki JM, Prigge ST, Caridha D, Chiang PK

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

Proteins

Bujnicki JM, Albert MA, Nelson DJ, Thurlow DL

Fold recognition, homology modeling, docking simulations, kinetics analysis and mutagenesis of ATP/CTP:tRNA nucleotidyltransferase from Methanococcus jannaschii.

Proteins

Bujnicki JM

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

Curr Protein Pept Sci

Coker JA, Sheridan PP, Loveland-Curtze J, Gutshall KR, Auman AJ, Brenchley JE

Biochemical characterization of a beta-galactosidase with a low temperature optimum obtained from an Antarctic arthrobacter isolate.

J Bacteriol

Coker JA, Sheridan PP, Loveland-Curtze J, Gutshall KR, Auman AJ, Brenchley JE

Biochemical characterization of a beta-galactosidase with a low temperature optimum obtained from an Antarctic arthrobacter isolate.

J Bacteriol

Zhang P, Nicholson DE, Bujnicki JM, Su X, Brendle JJ, Ferdig M, Kyle DE, Milhous WK, Chiang PK

Angiogenesis inhibitors specific for methionine aminopeptidase 2 as drugs for malaria and leishmaniasis

J Biomed Sci

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

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

J Biol Chem

Pintard L, Lecointe F, Bujnicki JM, Bonnerot C, Grosjean H, Lapeyre B

Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop

EMBO J

Pintard L, Bujnicki JM, Lapeyre B, Bonnerot C

MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase

EMBO J

Pingoud V, Kubareva E, Stengel G, Friedhoff P, Bujnicki JM, Urbanke C, Sudina A, Pingoud A

Evolutionary relationship between different subgroups of restriction endonucleases.

J Biol Chem

Godlewska R, Bujnicki JM, Ostrowski J, Jagusztyn-Krynicka EK

The hppA gene of Helicobacter pylori encodes the class C acid phosphatase precursor

FEBS Lett

Bujnicki J, Rychlewski L, Fischer D

Fold-recognition detects an error in the Protein Data Bank

Bioinformatics

Bujnicki JM, Rychlewski L

In silico identification, structure prediction and phylogenetic analysis of the 2'-O-ribose (cap 1) methyltransferase domain in the large structural protein of ssRNA negative-strand viruses

Protein Eng

Bujnicki JM, Rychlewski L

RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited--bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure

BMC Bioinformatics

Bujnicki JM, Rychlewski L

Fold-recognition analysis predicts that the Tag protein family shares a common domain with the helix-hairpin-helix DNA glycosylases

DNA Repair (Amst)

Bujnicki JM, Leach RA, Debski J, Rychlewski L

Bioinformatic analyses of the tRNA: (guanine 26, N2,N2)-dimethyltransferase (Trm1) family

J Mol Microbiol Biotechnol

Bujnicki JM, Feder M, Rychlewski L, Fischer D

Errors in the D. radiodurans large ribosomal subunit structure detected by protein fold-recognition and structure validation tools

FEBS Lett

Bujnicki JM, Feder M, Radlinska M, Blumenthal RM

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

J Mol Evol

Bujnicki JM, Blumenthal RM, Rychlewski L

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

J Mol Microbiol Biotechnol

Bujnicki JM

Sequence permutations in the molecular evolution of DNA methyltransferases

BMC Evol Biol

Radlinska M, Bujnicki JM

Site-directed mutagenesis defines the catalytic aspartate in the active site of the atypical DNA: m4C methyltransferase M.NgoMXV

Acta Microbiol Pol

Radlinska M, Bujnicki JM

Cloning of enterohemorrhagic Escherichia coli phage VT-2 dam methyltransferase

Acta Microbiol Pol

Lundström J, Rychlewski L, Bujnicki J, Elofsson A

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

Protein Sci

Bujnicki JM, Rychlewski L

The herpesvirus alkaline exonuclease belongs to the restriction endonuclease PD-(D/E)XK superfamily: insight from molecular modeling and phylogenetic analysis.

Virus Genes

Bujnicki JM, Rychlewski L

Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles.

J Mol Microbiol Biotechnol

Bujnicki JM, Rychlewski L

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

Genome Biol

Bujnicki JM, Rychlewski L

Unusual evolutionary history of the tRNA splicing endonuclease EndA: relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases.

Protein Sci

Bujnicki JM, Rychlewski L

Identification of a PD-(D/E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs

Gene

Bujnicki JM, Rychlewski L

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

Acta Microbiol Pol

Bujnicki JM, Rotkiewicz P, Kolinski A, Rychlewski L

Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics.

Protein Eng

Bujnicki JM, Radlinska M, Zaleski P, Piekarowicz A

Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage

Acta Biochim Pol

Bujnicki JM, Radlinska M, Rychlewski L

Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed

Trends Biochem Sci

Bujnicki JM, Radlinska M

Cloning and characterization of M.LmoA118I, a novel DNA:m4C methyltransferase from the Listeria monocytogenes phage A118, a close homolog of M.NgoMXV

Acta Microbiol Pol

Bujnicki JM, Feder M, Radlinska M, Rychlewski L

mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships

BMC Bioinformatics

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

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

Proteins

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

LiveBench-1: continuous benchmarking of protein structure prediction servers

Protein Sci

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

Structure prediction meta server

Bioinformatics

Bujnicki JM

A model of structure and action of Sau3AI restriction endonuclease that comprises two MutH-like endonuclease domains within a single polypeptide.

Acta Microbiol Pol

Bujnicki JM

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

Acta Biochim Pol

Bujnicki JM

In silico analysis of the tRNA:m1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea

FEBS Lett

Bujnicki JM, Rychlewski L

Prediction of a common fold for all four subunits of the yeast tRNA splicing endonuclease: implications for the evolution of the EndA/Sen family.

FEBS Lett

Bujnicki JM, Rychlewski L

Prediction of a novel RNA 2'-O-ribose methyltransferase subfamily encoded by the Escherichia coli YgdE open reading frame and its orthologs

Acta Microbiol Pol

Bujnicki JM, Radlinska M, Rychlewski L

Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc finger and structural similarity to betabetaalphaMe endonucleases

Mol Microbiol

Bujnicki JM

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

Acta Microbiol Pol

Bujnicki JM

Phylogenomic analysis of 16S rRNA:(guanine-N2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino-methyltransferases.

FASEB J