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List of works by Janusz Bujnicki

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

scientific article
GeneSilico protein structure prediction meta-server

scientific article
Transcriptome profile of human colorectal adenomas

scientific article published in December 2007
MODOMICS: a database of RNA modification pathways. 2017 update

scientific article published on 2 November 2017
Pcons: a neural-network-based consensus predictor that improves fold recognition

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

scientific article
MODOMICS: a database of RNA modification pathways. 2008 update

scientific article published on 14 October 2008
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
MetaMQAP: a meta-server for the quality assessment of protein models

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

scientific article published on 23 February 2012
MODOMICS: a database of RNA modification pathways

scientific article published in January 2006
ModeRNA: a tool for comparative modeling of RNA 3D structure

scientific article published on February 7, 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
Streptococcal Scl1 and Scl2 proteins form collagen-like triple helices

scientific article published on 25 April 2002
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases

scientific article published on 5 March 2007
Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB

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

scientific article
The YTH domain is a novel RNA binding domain

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

scientific article published on 16 April 2015
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
Phylogenomic analysis of the GIY-YIG nuclease superfamily

scientific article published on 28 April 2006
Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases

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

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

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

scientific article published on 2 May 2008
Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA

scientific article
Computational methods for prediction of protein-RNA interactions

scientific article published on 12 October 2011
Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits

scientific article
RNAcentral: an international database of ncRNA sequences

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

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

scientific article published on 23 November 2004
RNAcentral: a comprehensive database of non-coding RNA sequences

scientific article (publication date: 4 January 2017)
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure

scientific article
LiveBench-1: continuous benchmarking of protein structure prediction servers

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

scientific article
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

scientific article published on 01 February 2002
DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking

scientific article published on August 18, 2011
Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria

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

scientific article published on 23 January 2014
The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein

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

scientific article
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
Distribution and frequencies of post-transcriptional modifications in tRNAs

scientific article published on January 1, 2014
Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases

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

scientific article published in January 2005
NPDock: a web server for protein-nucleic acid docking

scientific article
Phylogenetic analysis of haloalkane dehalogenases

scientific article published in May 2007
Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models

scientific article
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

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