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1

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

Nowacka, Martyna, Boccaletto, Pietro, Jankowska, Elzbieta, Jarzynka, Tomasz, Bujnicki, Janusz M, Dunin-Horkawicz, Stanislaw

Journal:

Year:

2019

Language:

english

File:

PDF, 1.91 MB

english, 2019

2

Predicting Atomic Details of the Unfolding Pathway for YibK, a Knotted Protein from the SPOUT Superfamily

Tuszynska, Irina, Bujnicki, Janusz M.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2010

Language:

english

File:

PDF, 1.83 MB

english, 2010

3

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

Gordana Maravić Vlahoviček, Sonja Čubrilo, Karolina L. Tkaczuk, Janusz M. Bujnicki

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2008

Language:

english

File:

PDF, 1.78 MB

english, 2008

4

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

Richard K. Gordon, Krzysztof Ginalski, Witold R. Rudnicki, Leszek Rychlewski, Marvin C. Pankaskie, Janusz M. Bujnicki, Peter K. Chiang

Journal:

Year:

2003

Language:

english

File:

PDF, 459 KB

english, 2003

5

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

Jan Kosinski, Iwona A. Cymerman, Marcin Feder, Michal A. Kurowski, Joanna M. Sasin, Janusz M. Bujnicki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 897 KB

english, 2003

6

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

Iwona A. Cymerman, Agnieszka Obarska, Krzysztof J. Skowronek, Arvydas Lubys, Janusz M. Bujnicki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 464 KB

english, 2006

7

LiveBench-1: Continuous benchmarking of protein structure prediction servers

Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer, Leszek Rychlewski

Journal:

Protein Science

Year:

2001

Language:

english

File:

PDF, 694 KB

english, 2001

8

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

Magnus, Marcin, Matelska, Dorota, Łach, Grzegorz, Chojnowski, Grzegorz, Boniecki, Michal J, Purta, Elzbieta, Dawson, Wayne, Dunin-Horkawicz, Stanislaw, Bujnicki, Janusz M

Journal:

Year:

2014

Language:

english

File:

PDF, 1.59 MB

english, 2014

9

Erratum to: Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of aThermussp. enzyme family

Agnieszka Zylicz-Stachula,Janusz M Bujnicki,Piotr M Skowron

Journal:

BMC Molecular Biology

Year:

2014

Language:

english

File:

PDF, 4.63 MB

english, 2014

10

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

Nithin, Chandran, Ghosh, Pritha, Bujnicki, Janusz

Journal:

Year:

2018

Language:

english

File:

PDF, 2.33 MB

english, 2018

11

Structural characterization of two tandemly arranged DNA methyltransferase genes from Neisseria gonorrhoeae MS11: N4-cytosine specific M.NgoMXV and nonfunctional 5-cytosine-type M.NgoMorf2P

Monika Radlinska, Janusz M. Bujnicki, Andrzej Piekarowicz

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 653 KB

english, 1999

12

Protein-Structure Prediction by Recombination of Fragments

Janusz M. Bujnicki

Journal:

Year:

2006

Language:

english

File:

PDF, 349 KB

english, 2006

13

Protein Structure Prediction: Concepts and Applications. Anna Tramontano.

Janusz Bujnicki

Journal:

Year:

2006

Language:

english

File:

PDF, 61 KB

english, 2006

14

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

Marcin Feder, Elzbieta Purta, Lukasz Koscinski, Sonja Čubrilo, Gordana Maravic Vlahovicek, Janusz M. Bujnicki

Journal:

Year:

2008

Language:

english

File:

PDF, 361 KB

english, 2008

15

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

Jan Kosinski, Inga Hinrichsen, Janusz M. Bujnicki, Peter Friedhoff, Guido Plotz

Journal:

Year:

2010

Language:

english

File:

PDF, 423 KB

english, 2010

16

“4D Biology for health and disease” workshop report

Jan-Pieter Abrahams, Rolf Apweiler, Rudi Balling, Michela G. Bertero, Janusz M. Bujnicki, Naomi E. Chayen, Patrick Chène, Gary L. Corthals, Tomasz Dyląg, Friedrich Förster, Albert J.R. Heck, Peter J.F

Journal:

New Biotechnology

Year:

2011

Language:

english

File:

PDF, 94 KB

english, 2011

17

Casein kinases phosphorylate multiple residues spanning the entire hnRNP K length

Michał Mikula, Jakub Karczmarski, Artur Dzwonek, Tymon Rubel, Ewa Hennig, Michał Dadlez, Janusz M. Bujnicki, Karol Bomsztyk, Jerzy Ostrowski

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2006

Language:

english

File:

PDF, 516 KB

english, 2006

18

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

Kommireddy Vasu, Matheshwaran Saravanan, Janusz M. Bujnicki, Valakunja Nagaraja

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2008

Language:

english

File:

PDF, 652 KB

english, 2008

19

Theoretical predictions of the impact of the trisubstituted pyrophosphate internucleotide bond on B DNA fragments

Bogusław Śmiech, Rajmund Kaźmierkiewicz, Janusz Bujnicki, Bernard Lammek

Journal:

Journal of Molecular Structure: THEOCHEM

Year:

2005

Language:

english

File:

PDF, 449 KB

english, 2005

20

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

Janusz M. Bujnicki, Monika Radlinska, Leszek Rychlewski

Journal:

Molecular Microbiology

Year:

2000

Language:

english

File:

PDF, 124 KB

english, 2000

21

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

Irina Tuszynska, Janusz M Bujnicki

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 1.09 MB

english, 2011

22

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

Agnieszka Zylicz-Stachula, Janusz M Bujnicki, Piotr M Skowron

Journal:

BMC Molecular Biology

Year:

2009

Language:

english

File:

PDF, 6.46 MB

english, 2009

23

TheyfhQgene ofEscherichia coliencodes a tRNA:Cm32/Um32 methyltransferase

Elzbieta Purta, Françoise van Vliet, Karolina L Tkaczuk, Stanislaw Dunin-Horkawicz, Hirotada Mori, Louis Droogmans, Janusz M Bujnicki

Journal:

BMC Molecular Biology

Year:

2006

Language:

english

File:

PDF, 1.98 MB

english, 2006

24

A homology model of restriction endonuclease SfiI in complex with DNA

Agnieszka A Chmiel, Janusz M Bujnicki, Krzysztof J Skowronek

Journal:

BMC Structural Biology

Year:

2005

Language:

english

File:

PDF, 3.51 MB

english, 2005

25

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

Katarzyna H Kaminska, Mikihiko Kawai, Michal Boniecki, Ichizo Kobayashi, Janusz M Bujnicki

Journal:

BMC Structural Biology

Year:

2008

Language:

english

File:

PDF, 4.78 MB

english, 2008

26

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

Marcin Pierechod, Agnieszka Nowak, Anna Saari, Elzbieta Purta, Janusz M. Bujnicki, Igor Konieczny

Journal:

Protein Science

Year:

2009

Language:

english

File:

PDF, 517 KB

english, 2009

27

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

Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer, Leszek Rychlewski

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 79 KB

english, 2001

28

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

Janusz M. Bujnicki, Megan A. Albert, Donald J. Nelson, David L. Thurlow

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 1017 KB

english, 2003

29

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

Janusz M. Bujnicki, Sean T. Prigge, Diana Caridha, Peter K. Chiang

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 862 KB

english, 2003

30

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

Monika Radlinska, Aneta Kondrzycka-Dada, Andrzej Piekarowicz, Janusz M. Bujnicki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 476 KB

english, 2005

31

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

Elżbieta Purta, Françoise van Vliet, Catherine Tricot, Lara G. De Bie, Marcin Feder, Krzysztof Skowronek, Louis Droogmans, Janusz M. Bujnicki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 479 KB

english, 2005

32

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

Andrzej Koliński, Janusz M. Bujnicki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 988 KB

english, 2005

33

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

Krzysztof J. Skowronek, Jan Kosinski, Janusz M. Bujnicki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 551 KB

english, 2006

34

Phylogenetic analysis of haloalkane dehalogenases

Eva Chovancová, Jan Kosinski, Janusz M. Bujnicki, Jiří Damborský

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 937 KB

english, 2007

35

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

Jan Kosinski, Elena Kubareva, Janusz M. Bujnicki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 885 KB

english, 2007

36

Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms2io6A37 in tRNA

Katarzyna H. Kaminska, Urszula Baraniak, Michal Boniecki, Katarzyna Nowaczyk, Anna Czerwoniec, Janusz M. Bujnicki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.31 MB

english, 2008

37

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

Martine Roovers, Yamina Oudjama, Katarzyna H. Kaminska, Elzbieta Purta, Joël Caillet, Louis Droogmans, Janusz M. Bujnicki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.02 MB

english, 2008

38

Angiogenesis inhibitors specific for methionine aminopeptidase 2 as drugs for Malaria and Leishmaniasis

Peng Zhang, Diarmuid E. Nicholson, Janusz M. Bujnicki, Xinzhuan Su, James J. Brendle, Michael Ferdig, Dennis E. Kyle, Wilbur K. Milhous, Peter K. Chiang

Journal:

Journal of Biomedical Science

Year:

2002

Language:

english

File:

PDF, 2.74 MB

english, 2002

39

Structure Prediction and Phylogenetic Analysis of a Functionally Diverse Family of Proteins Homologous to the MT-A70 Subunit of the Human mRNA:m6A Methyltransferase

Janusz M. Bujnicki, Marcin Feder, Monika Radlinska, Robert M. Blumenthal

Journal:

Journal of Molecular Evolution

Year:

2002

Language:

english

File:

PDF, 1.11 MB

english, 2002

40

Phylogeny of the Restriction Endonuclease-Like Superfamily Inferred from Comparison of Protein Structures

Janusz M. Bujnicki

Journal:

Journal of Molecular Evolution

Year:

2000

Language:

english

File:

PDF, 61 KB

english, 2000

41

Modeling ofEscherichia coliEndonuclease V structure in complex with DNA

Karolina A. Majorek, Janusz M. Bujnicki

Journal:

Journal of Molecular Modeling

Year:

2009

Language:

english

File:

PDF, 595 KB

english, 2009

42

RNA and protein 3D structure modeling: similarities and differences

Kristian Rother, Magdalena Rother, Michał Boniecki, Tomasz Puton, Janusz M. Bujnicki

Journal:

Journal of Molecular Modeling

Year:

2011

Language:

english

File:

PDF, 487 KB

english, 2011

43

SURF’s UP! — Protein classification by surface comparisons

Joanna M Sasin, Adam Godzik, Janusz M Bujnicki

Journal:

Journal of Biosciences

Year:

2007

Language:

english

File:

PDF, 219 KB

english, 2007

44

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

Runlin Han, Clayton C. Caswell, Ewa Lukomska, Douglas R. Keene, Marcin Pawlowski, Janusz M. Bujnicki, Jiyeun K. Kim, Slawomir Lukomski

Journal:

Molecular Microbiology

Year:

2006

Language:

english

File:

PDF, 574 KB

english, 2006

45

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

Elzbieta Purta, Michelle O'Connor, Janusz M. Bujnicki, Stephen Douthwaite

Journal:

Molecular Microbiology

Year:

2009

Language:

english

File:

PDF, 489 KB

english, 2009

46

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

Mária Pukáncsik, Angéla Békési, Éva Klement, Éva Hunyadi-Gulyás, Katalin F. Medzihradszky, Jan Kosinski, Janusz M. Bujnicki, Carlos Alfonso, Germán Rivas, Beáta G. Vértessy

Journal:

Year:

2010

Language:

english

File:

PDF, 980 KB

english, 2010

47

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

Pukszta, Sebastian, Schilke, Brenda, Dutkiewicz, Rafal, Kominek, Jacek, Moczulska, Kaja, Stepien, Barbara, Reitenga, Krista G, Bujnicki, Janusz M, Williams, Barry, Craig, Elizabeth A

Journal:

Year:

2010

Language:

english

File:

PDF, 796 KB

english, 2010

48

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

Gyrd-Hansen, Mads, Darding, Maurice, Miasari, Maria, Santoro, Massimo M., Zender, Lars, Xue, Wen, Tenev, Tencho, da Fonseca, Paula C.A., Zvelebil, Marketa, Bujnicki, Janusz M.

Journal:

Nature Cell Biology

Year:

2008

Language:

english

File:

PDF, 6.45 MB

english, 2008

49

The Herpesvirus Alkaline Exonuclease Belongs to the Restriction Endonuclease PD-(D/E)XK Superfamily: Insight from Molecular Modeling and Phylogenetic Analysis

Janusz M. Bujnicki, Leszek Rychlewski

Journal:

Year:

2001

Language:

english

File:

PDF, 234 KB

english, 2001

50

Is the HemK Family of Putative S-Adenosylmethionine-Dependent Methyltransferases a “Missing” zeta Subfamily of Adenine Methyltransferases? A Hypothesis

Janusz M. Bujnicki, Monika Radlinska

Journal:

Year:

1999

Language:

english

File:

PDF, 143 KB

english, 1999