Janusz M Bujnicki

发表

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

Chris Bailey-Kellogg, Xiaoduan Ye, Patrick K O'Neil, 2004, Protein science : a publication of the Protein Society.

Janusz M Bujnicki, Kristian Rother, Magdalena Rother, 2014, Methods in molecular biology.

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

Marcin Feder, Jan Kosinski, Michal A Kurowski, 2003, Proteins.

RNAcentral: an international database of ncRNA sequences

Hsien-Da Huang, Alex Bateman, Janusz M Bujnicki, 2014, Nucleic Acids Res..

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

Janusz M Bujnicki, Piotr Formanowicz, Marcin Radom, 2019, PloS one.

Suffix techniques as a rapid method for RNA substructure search.

Janusz M Bujnicki, Robert Preissner, Kristian Rother, 2008, Genome informatics. International Conference on Genome Informatics.

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

Marcin Feder, Michal J Gajda, Jan Kosinski, 2005, Proteins.

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

Janusz M Bujnicki, Andrzej Koliński, A. Kolinski, 2005, Proteins.

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

Janusz M Bujnicki, Joanna M. Kasprzak, Marcin Magnus, 2016, Methods in molecular biology.

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.

Leszek Rychlewski, Janusz M Bujnicki, R. Blumenthal, 2002, Journal of molecular microbiology and biotechnology.

Computational modeling of protein-RNA complex structures.

Janusz M Bujnicki, Irina Tuszynska, Joanna M. Kasprzak, 2014, Methods.

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

Alfred Pingoud, Janusz M Bujnicki, Iwona A Cymerman, 2004, Journal of molecular biology.

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

Leszek Rychlewski, Marcin Feder, Janusz M Bujnicki, 2002, FEBS letters.

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

Jakub Pas, Marcin Feder, Janusz M Bujnicki, 2003, Gene.

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.

Leszek Rychlewski, Janusz M Bujnicki, J. Bujnicki, 2002, Protein engineering.

Mva1269I: A Monomeric Type IIS Restriction Endonuclease from Micrococcus Varians with Two EcoRI- and FokI-like Catalytic Domains*

Janusz M Bujnicki, J. Bujnicki, J. Kosiński, 2005, Journal of Biological Chemistry.

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

Janusz M Bujnicki, Johan Wouters, Henri Grosjean, 2004, Nucleic acids research.

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

Janusz M Bujnicki, Stanislaw Dunin-Horkawicz, J. Bujnicki, 2015, eLife.

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

Alex Bateman, Guy Cochrane, Janusz M Bujnicki, 2018, Nucleic Acids Res..

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

Feng Ding, Kristian Rother, Thomas Hermann, 2012, RNA.

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

Janusz M Bujnicki, Valakunja Nagaraja, Iwona A Cymerman, 2004, Nucleic acids research.

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

Marcin Feder, Janusz M Bujnicki, J. Bujnicki, 2005, BMC Genomics.

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

Marcin Feder, Janusz M Bujnicki, Dominik Gront, 2007, BMC Structural Biology.

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

Janusz M Bujnicki, Karolina L Tkaczuk, J. Bujnicki, 2008, Biochimica et biophysica acta.

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

Janusz M Bujnicki, Pritha Ghosh, Chandran Nithin, 2018, Genes.

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

Janusz M Bujnicki, Grzegorz Chojnowski, Trushar R Patel, 2017, PloS one.

Phylogenomic analysis of the GIY-YIG nuclease superfamily

Marcin Feder, Janusz M Bujnicki, Stanislaw Dunin-Horkawicz, 2006, BMC Genomics.

Protein‐Structure Prediction by Recombination of Fragments

Janusz M Bujnicki, J. Bujnicki, 2006, Chembiochem : a European journal of chemical biology.

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

Janusz M Bujnicki, J. Bujnicki, 2003, Current protein & peptide science.

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

Alfred Pingoud, Janusz M Bujnicki, J. Bujnicki, 2003, Biochemistry.

Distribution and frequencies of post-transcriptional modifications in tRNAs

Janusz M Bujnicki, Henri Grosjean, Anna Olchowik, 2014, RNA biology.

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

Janusz M Bujnicki, Elzbieta Purta, Katarzyna H. Kaminska, 2008, Proteins.

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

Leszek Rychlewski, Janusz M Bujnicki, Witold R Rudnicki, 2003, European journal of biochemistry.

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

Janusz M Bujnicki, Tomasz Waleń, Grzegorz Chojnowski, 2014, Nucleic acids research.

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

Janusz M Bujnicki, Marcin Magnus, Wayne Dawson, 2014, RNA biology.

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

Janusz M Bujnicki, Heping Zheng, Wladek Minor, 2015, Nucleic acids research.

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

Janusz M Bujnicki, Michal Boniecki, Ichizo Kobayashi, 2008, BMC Structural Biology.

SURF’s UP! — Protein classification by surface comparisons

Janusz M Bujnicki, Adam Godzik, Joanna M Sasin, 2007, Journal of Biosciences.

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

Janusz M Bujnicki, Tomasz Zok, Jakub Wiedemann, 2019, Nucleic acids research.

The YTH Domain Is a Novel RNA Binding Domain*

Michael Hiller, Janusz M Bujnicki, Rainer Pudimat, 2010, The Journal of Biological Chemistry.

Computational modeling of RNA 3D structures and interactions.

Janusz M Bujnicki, J. Bujnicki, W. Dawson, 2016, Current opinion in structural biology.

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

Janusz M Bujnicki, Peter Friedhoff, Jan Kosinski, 2005, Journal of molecular biology.

Trm7p catalyses the formation of two 2′‐O‐methylriboses in yeast tRNA anticodon loop

Janusz M Bujnicki, Henri Grosjean, J. Bujnicki, 2002, The EMBO journal.

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

Feng Ding, Jian Wang, Janusz M Bujnicki, 2015, RNA.

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

Janusz M Bujnicki, Jan Kosinski, J. Bujnicki, 2007, Proteins.

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

Janusz M Bujnicki, Albrecht Bindereif, Henning Urlaub, 2009, Genes & development.

Virtual Screening and Experimental Verification to Identify Potential Inhibitors of the ErmC Methyltransferase Responsible for Bacterial Resistance against Macrolide Antibiotics

Marcin Feder, Janusz M Bujnicki, Elzbieta Purta, 2008, ChemMedChem.

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

Taner Z Sen, Andrzej Kloczkowski, Robert L Jernigan, 2008, Biophysical journal.

RNAcentral: a comprehensive database of non-coding RNA sequences

Alex Bateman, Eva Huala, Guy Cochrane, 2016, Nucleic acids research.

LigandRNA: computational predictor of RNA–ligand interactions

Janusz M Bujnicki, Kaja Milanowska, Anna Philips, 2013, RNA.

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

Janusz M Bujnicki, Katarzyna H. Kaminska, J. Bujnicki, 2008, Cell cycle.

Sequence permutations in the molecular evolution of DNA methyltransferases

Janusz M Bujnicki, J. Bujnicki, 2002, BMC Evolutionary Biology.

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

Janusz M Bujnicki, Iwona A Cymerman, Agnieszka Obarska, 2006, Proteins.

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

Feng Ding, Janusz M Bujnicki, Lin Huang, 2020, RNA.