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List of works by Janusz Bujnicki

"4D Biology for health and disease" workshop report

scientific article published on 15 October 2010

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

scientific article published in June 2011

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 ⬇️

scientific article published on January 1, 2003

A Single Zinc Ion Is Sufficient for an Active Trypanosoma brucei tRNA Editing Deaminase ⬇️

scientific article published on April 20, 2011

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

scientific article

A homology model of restriction endonuclease SfiI in complex with DNA

scientific article

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

scientific article published in July 2007

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

article

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

scientific article published in November 2012

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

scientific article

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

scientific article published on 22 April 2005

A toolbox for developing bioinformatics software

scientific article published on 29 July 2011

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

scientific article published on January 2009

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

scientific article

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

scientific article published on 27 June 2015

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

scientific article published on 10 September 2015

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

scientific article published in August 2005

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

scientific article published on January 2002

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

scientific article published on 01 February 2021

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

scientific article published in September 2003

Asymmetric DNA methylation by dimeric EcoP15I DNA methyltransferase

scientific article

Automated modeling of RNA 3D structure

scientific article published on January 2014

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

scientific article

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

scientific article

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

scientific article

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

article

Bioinformatics and computational biology in Poland

scientific article (publication date: 2013)

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

scientific article

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

scientific article

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

scientific article

Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 29 May 2009

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

scientific article published on January 1, 2001

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

scientific article

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

scientific article published on January 2005

Cloning of enterohemorrhagic Escherichia coli phage VT-2 dam methyltransferase

scientific article published on January 1, 2001

Cloning of the Dam methyltransferase gene from Haemophilus influenzae bacteriophage HP1.

scientific article published on January 1999

Coarse-grained modeling of RNA 3D structure

scientific article published in July 2016

Common Design Principles in the Spliceosomal RNA Helicase Brr2 and in the Hel308 DNA Helicase

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

scientific article

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

scientific article (publication date: April 2013)

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

scientific article published on 18 March 2014

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

scientific article

Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models

scientific article published on 25 August 2022

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

scientific article published on 03 February 2015

Computational methods for prediction of protein-RNA interactions

scientific article published on 12 October 2011

Computational modeling of RNA 3D structure based on experimental data

scientific article published on 08 February 2019

Computational modeling of RNA 3D structures and interactions

scientific article published in April 2016

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

scientific article published on 23 April 2014

Computational modeling of protein-RNA complex structures

scientific article published in February 2014

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

scientific article published on March 2009

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

scientific article published on 10 October 2007

Correction: Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases.

scientific article published in January 2011

Crohn's disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation

scientific article

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

scientific article published in August 2012

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

scientific article

Crystal structure of a fructokinase homolog from Halothermothrix orenii

scientific article

Crystal structure of human Acinus RNA recognition motif domain

scientific article published in 2018

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

scientific article

Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life

scientific article published in June 2012

Crystallographic and Bioinformatic Studies on Restriction Endonucleases: Inference of Evolutionary Relationships in the “Midnight Zone” of Homology ⬇️

scientific article published on October 1, 2003

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

scientific article published on August 18, 2011

DEGRONOPEDIA: a web server for proteome-wide inspection of degrons

scientific article published in 2024

DNase II is a member of the phospholipase D superfamily

scientific article published on 8 September 2005

Databases and bioinformatics tools for the study of DNA repair

scientific article published on 14 July 2011

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

scientific article published on 14 March 2017

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

scientific article published on 20 June 2012

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

scientific article published on 30 September 2014

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

scientific article

Distribution and frequencies of post-transcriptional modifications in tRNAs

scientific article

EXOG, a novel paralog of Endonuclease G in higher eukaryotes

scientific journal article

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

scientific article

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

scientific article published on 19 April 2011

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

scientific article published on 19 April 2018

Evolutionary relationship between different subgroups of restriction endonucleases

scientific article published in Journal of Biological Chemistry

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

scientific article

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

scientific article published on October 17, 2010

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

scientific article published in January 2005

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

scientific article published in 2014

First Steps of Protein Structure Prediction

scientific article

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

scientific article

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

scientific article

Fold-recognition detects an error in the Protein Data Bank

scientific article

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

scientific article published on 7 November 2008

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

scientific article published in May 2006

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

scientific article

GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function

scientific article

GeneSilico protein structure prediction meta-server.

scientific article

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

scientific article

Genetic characterisation of the cjaAB operon of Campylobacter coli.

scientific article published in January 2006

Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements

scientific article published on 10 November 2020

Geometric analysis of cross-linkability for protein fold discrimination.

scientific article

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

scientific article published on January 2001

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

scientific article published in December 2004

Homology modelling of the DNA 5mC methyltransferase M.BssHII. Is permutation of functional subdomains common to all subfamilies of DNA methyltransferases?

scientific article published in June 2000

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

scientific article

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

scientific article published on 5 November 2018

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

scientific article published on January 2007

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

scientific article published on 22 January 2007

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

scientific article published on 19 October 2008

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

scientific article published on October 15, 2011

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

scientific article published in August 2010

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

scientific article published in April 2001

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

scientific article

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

scientific article

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

scientific article

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

scientific article published in December 2006

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 07 December 2016

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

scientific article published on 20 October 2017

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

scientific article published on October 26, 2001

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

scientific article

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

scientific article

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

scientific article published on 22 October 2009

Intrinsic Disorder in the Human Spliceosomal Proteome ⬇️

scientific article published on August 9, 2012

Is AID a monomer in solution?

scientific article

LigandRNA: computational predictor of RNA-ligand interactions

scientific article published on 21 October 2013

LiveBench-1: continuous benchmarking of protein structure prediction servers

scientific article

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

scientific article

Loss of Conserved Noncoding RNAs in Genomes of Bacterial Endosymbionts

scientific article published on 18 January 2016

MODOMICS: a database of RNA modification pathways

scientific article published in January 2006

MODOMICS: a database of RNA modification pathways--2013 update

scientific article

MODOMICS: a database of RNA modification pathways. 2008 update

scientific article published on 14 October 2008

MODOMICS: a database of RNA modification pathways. 2017 update

scientific article published on 2 November 2017

MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase

scientific article

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

scientific article

Malaria: therapy, genes and vaccines

scientific article published in May 2006

Matching tRNA modifications in humans to their known and predicted enzymes

scientific article published on 18 March 2019

Medaka: a promising model animal for comparative population genomics

scientific article

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

scientific article

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

scientific article published in December 2012

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

scientific article

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

scientific article published on 21 November 2011

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

scientific article published on 4 July 2011

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

scientific article published on February 7, 2011

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

scientific article

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

scientific article

Modeling of Protein-RNA Complex Structures Using Computational Docking Methods

scientific article published in January 2016

Modeling of ribonucleic acid-ligand interactions

scientific article published on 14 September 2015

Molecular evolution of DNA-(cytosine-N4) methyltransferases: evidence for their polyphyletic origin

scientific article

Molecular evolution of dihydrouridine synthases

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published in September 2003

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

scientific article

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

scientific article published on 20 June 2017

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

scientific article

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

scientific article

NPDock: a web server for protein-nucleic acid docking

scientific article

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

scientific article

Novel highly thermostable endolysin from Thermus scotoductus MAT2119 bacteriophage Ph2119 with amino acid sequence similarity to eukaryotic peptidoglycan recognition proteins

scientific article

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

scientific article published on 6 January 2018

Novel insights from structural analysis of lentiviral and gammaretroviral reverse transcriptases in complex with RNA/DNA hybrids

scientific article published on 19 September 2013

Novel non-specific DNA adenine methyltransferases

scientific article published on 18 November 2011

ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 13 September 2019

Phylogenetic analysis of haloalkane dehalogenases

scientific article published in May 2007

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

scientific article

Phylogenomic analysis of the GIY-YIG nuclease superfamily

scientific article published on 28 April 2006

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

scientific article

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

scientific article published on 23 October 2015

Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures

scientific article published on 01 January 2000

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

scientific article published in February 2010

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

scientific article

Positioning Europe for the EPITRANSCRIPTOMICS challenge.

scientific article published on 19 April 2018

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

scientific article published on 4 January 2008

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

scientific article published in December 2000

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

scientific article

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

scientific article published in December 2004

Protein-structure prediction by recombination of fragments.

scientific article

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

scientific article

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

scientific article published on 21 May 2013

REPAIRtoire--a database of DNA repair pathways

scientific article

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

scientific article published on 11 January 2012

RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS.

scientific article published in January 2016

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

scientific article

RNA and protein 3D structure modeling: similarities and differences ⬇️

scientific article published on January 22, 2011

RNA methyltransferases involved in 5' cap biosynthesis

scientific article

RNA tertiary structure prediction with ModeRNA ⬇️

scientific article published on September 6, 2011

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

scientific article published on 16 April 2015

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

scientific article

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

scientific article published on 05 May 2020

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

scientific article published on 01 January 2020

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

scientific article published on 23 February 2012

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

scientific article

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

scientific article published on 06 June 2020

RNAcentral: A vision for an international database of RNA sequences

scientific article (publication date: November 2011)

RNAcentral: a comprehensive database of non-coding RNA sequences

scientific article (publication date: 4 January 2017)

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

scientific article published on 5 November 2018

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

scholarly article published in Nucleic Acids Research

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

scientific article published on 25 April 2013

RNApathwaysDB--a database of RNA maturation and decay pathways

scientific article (publication date: 2013)

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

scientific article published on 23 October 2017

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

Rational engineering of sequence specificity in R.MwoI restriction endonuclease

scientific article

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

scientific article

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

scientific article published on 10 April 2012

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

scientific article published on 26 August 2013

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

scientific article published on July 2009

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

scientific article published on July 12, 2011

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

scientific article

SURF'S UP! - protein classification by surface comparisons

scientific article published in January 2007

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

scientific article published on January 1, 2002

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

scientific article published on January 2001

Sequence permutations in the molecular evolution of DNA methyltransferases

scientific article published on 12 March 2002

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

scientific article

Sequence-specific cleavage of dsRNA by Mini-III RNase

scientific article

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

scientific article

Sequence-specific endoribonucleases

scientific article published on January 2016

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

scientific article published on June 2008

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

scientific article

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

scientific article published in May 2005

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

scientific article

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

scientific article

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

scientific article published on 19 April 2016

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

scientific article published on January 1, 2001

Solution conformation of adenovirus virus associated RNA-I and its interaction with PKR.

scientific article published on 28 November 2013

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

scientific article published on 24 November 2004

Statins impair glucose uptake in human cells

scientific article published on 26 April 2014

Statins impair glucose uptake in tumor cells

scientific article published in April 2012

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

scientific article

Streptococcal Scl1 and Scl2 proteins form collagen-like triple helices

scientific article published on 25 April 2002

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

scientific article

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

scientific article

Structural and degradative aspects of ornithine decarboxylase antizyme inhibitor 2.

scientific article published on 2 June 2014

Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases

scientific article published on 5 March 2007

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

scientific article published on 2 May 2008

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

scientific article published in April 2004

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

scientific article published on 15 December 2015

Structural bases of peptidoglycan recognition by lysostaphin SH3b domain

scientific article published on 12 April 2019

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 ⬇️

scientific article published on November 9, 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

scientific article

Structural basis of the methylation specificity of R.DpnI

scientific article

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

scientific article published in January 2008

Structural bioinformatics of the human spliceosomal proteome

scientific article published on 9 May 2012

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

scientific article published on 13 April 2006

Structure Prediction for Alternatively Spliced Proteins

Structure and Evolutionary Origin of Ca2+-Dependent Herring Type II Antifreeze Protein

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published in September 2003

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

scientific article published in September 2017

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

scientific article published on 10 May 2006

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

scientific article published on 2 July 2007

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

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

scientific article published on 12 July 2005

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

scientific article published on 28 June 2008

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

scientific article published on 23 January 2014

The Signature of the Five-Stranded vRRM Fold Defined by Functional, Structural and Computational Analysis of the hnRNP L Protein

scientific article

The Structure of Sucrose Phosphate Synthase from Halothermothrix orenii Reveals Its Mechanism of Action and Binding Mode

scientific article

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

scientific article published on 29 November 2007

The YTH domain is a novel RNA binding domain

scientific article

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

scientific journal article

The architecture of the Schizosaccharomyces pombe CCR4-NOT complex

scientific article published on 25 January 2016

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

scientific article

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

scientific article published in March 2001

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

scientific article published on 15 February 2012

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

scientific article

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

scientific article published on November 5, 2012

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

scientific article published on 6 January 2006

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

scientific article

The yggH Gene of Escherichia coli Encodes a tRNA (m 7 G46) Methyltransferase ⬇️

scientific article published on May 1, 2003

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

scientific article

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

scientific article published on October 1, 2001

Topological measurement of an A-tract bend angle: comparison of the bent and straightened states

scientific article

Transcriptome profile of human colorectal adenomas

scientific article published in December 2007

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

scientific article

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

scientific article

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

scientific article

Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site

scientific article

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

scientific article published on 23 November 2004

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

scientific article

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

scientific article

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

scientific article published in February 2008

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

scientific article published on 28 August 2008

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

scientific article

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

scientific article

fingeRNAt-A novel tool for high-throughput analysis of nucleic acid-ligand interactions

scientific article published on 02 June 2022

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

scientific article

tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs

scientific article published on 22 March 2016

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