Janusz Bujnicki: search on Z-Library

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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

Prediction of Protein Structures, Functions, and Interactions (Bujnicki/Prediction of Protein Structures, Functions, and Interactions) || First Steps of Protein Structure Prediction

Bujnicki, Janusz M.

Year:

2008

Language:

english

File:

PDF, 333 KB

english, 2008

4

Evaluation of Molecular Models for the Affinity Maturation of Antibodies: Roles of Cytosine Deamination by AID and DNA Repair

Samaranayake, Mala, Bujnicki, Janusz M., Carpenter, Michael, Bhagwat, Ashok S.

Journal:

Chemical Reviews

Year:

2006

Language:

english

File:

PDF, 933 KB

english, 2006

5

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

6

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

7

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

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

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

10

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

11

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

12

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

13

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

14

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

Janusz M Bujnicki, Leszek Rychlewski

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 874 KB

english, 2002

15

YccW is the m5C Methyltransferase Specific for 23S rRNA Nucleotide 1962

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

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 1.79 MB

english, 2008

16

Topological Measurement of an A-tract Bend Angle: Comparison of the Bent and Straightened States

Vladimir Tchernaenko, Monika Radlinska, Christopher Drabik, Janusz Bujnicki, Herbert R Halvorson, Leonard C Lutter

Journal:

Journal of Molecular Biology

Year:

2003

Language:

english

File:

PDF, 468 KB

english, 2003

17

Computational methods for prediction of protein–RNA interactions

Tomasz Puton, Lukasz Kozlowski, Irina Tuszynska, Kristian Rother, Janusz M. Bujnicki

Journal:

Journal of Structural Biology

Year:

2012

Language:

english

File:

PDF, 343 KB

english, 2012

18

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

Teck Khiang Chua, Janusz M. Bujnicki, Tien-Chye Tan, Frederick Huynh, Bharat K. Patel and J. Sivaraman

Journal:

Year:

2008

Language:

english

File:

PDF, 3.14 MB

english, 2008

19

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

Manfredonia, Ilaria, Nithin, Chandran, Ponce-Salvatierra, Almudena, Ghosh, Pritha, Wirecki, Tomasz K, Marinus, Tycho, Ogando, Natacha S, Snijder, EricÂ J, vanÂ Hemert, Martijn J, Bujnicki, Janusz M, I

Journal:

Nucleic Acids Research

Year:

2020

File:

PDF, 9.63 MB

2020

20

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

Patrick Schäfer, Iwona A. Cymerman, Janusz M. Bujnicki, Gregor Meiss

Journal:

Protein Science

Year:

2007

Language:

english

File:

PDF, 639 KB

english, 2007

21

Sequence permutations in the molecular evolution of DNA methyltransferases

Janusz M Bujnicki

Journal:

BMC Evolutionary Biology

Year:

2002

Language:

english

File:

PDF, 492 KB

english, 2002

22

Crystal Structure of the Escherichia coli 23S rRNA:m5C Methyltransferase RlmI (YccW) Reveals Evolutionary Links between RNA Modification Enzymes

S. Sunita, Karolina L. Tkaczuk, Elzbieta Purta, Joanna M. Kasprzak, Stephen Douthwaite, Janusz M. Bujnicki, J. Sivaraman

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 5.03 MB

english, 2008

23

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

Marcin Magnus, Marcin Pawlowski, Janusz M. Bujnicki

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2012

Language:

english

File:

PDF, 675 KB

english, 2012

24

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

25

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

26

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

Janusz M Bujnicki, Leszek Rychlewski, Monika Radlinska

Journal:

Trends in Biochemical Sciences

Year:

2001

Language:

english

File:

PDF, 53 KB

english, 2001

27

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

Journal:

Year:

2005

Language:

english

File:

PDF, 1.78 MB

english, 2005

28

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

Vladimir Pena, Sina Mozaffari Jovin, Patrizia Fabrizio, Jerzy Orlowski, Janusz M. Bujnicki, Reinhard Lührmann, Markus C. Wahl

Journal:

Year:

2009

Language:

english

File:

PDF, 2.04 MB

english, 2009

29

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

Janusz M Bujnicki

Journal:

Year:

2001

Language:

english

File:

PDF, 4.21 MB

english, 2001

30

Prediction of Protein Structures, Functions, and Interactions (Bujnicki/Prediction of Protein Structures, Functions, and Interactions) || The Basics of Protein Sequence Analysis

Bujnicki, Janusz M.

Year:

2008

Language:

english

File:

PDF, 560 KB

english, 2008

31

Virtual screening strategies in drug design – methods and applications

Bielska, Ewa, Lucas, Xavier, Czerwoniec, Anna, M. Kasprzak, Joanna, H. Kaminska, Katarzyna, M. Bujnicki, Janusz

Journal:

Year:

2011

Language:

english

File:

PDF, 785 KB

english, 2011

32

Computational modeling of RNA 3D structure based on experimental data

Ponce-Salvatierra, Almudena, --, Astha, Merdas, Katarzyna, Chandran, Nithin, Ghosh, Pritha, Mukherjee, Sunandan, Bujnicki, Janusz M

Journal:

Bioscience Reports

Year:

2019

File:

PDF, 6.99 MB

2019

33

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

34

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

Michal A Kurowski, Ashok S Bhagwat, Grzegorz Papaj, Janusz M Bujnicki

Journal:

Year:

2003

Language:

english

File:

PDF, 415 KB

english, 2003

35

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

Xingding Zhou, Teck Khiang Chua, Karolina L. Tkaczuk, Janusz M. Bujnicki, J. Sivaraman

Journal:

Journal of Structural Biology

Year:

2010

Language:

english

File:

PDF, 1.08 MB

english, 2010

36

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

Vera Pingoud, Charlotte Conzelmann, Steffen Kinzebach, Anna Sudina, Valeri Metelev, Elena Kubareva, Janusz M Bujnicki, Rudi Lurz, Gerhild Lüder, Shuang-Yong Xu, Alfred Pingoud

Journal:

Journal of Molecular Biology

Year:

2003

Language:

english

File:

PDF, 2.47 MB

english, 2003

37

Prediction of Protein Structures, Functions, and Interactions (Bujnicki/Prediction of Protein Structures, Functions, and Interactions) || Protein Function Prediction via Analysis of Interactomes

Bujnicki, Janusz M.

Year:

2008

Language:

english

File:

PDF, 351 KB

english, 2008

38

Prediction of Protein Structures, Functions, and Interactions (Bujnicki/Prediction of Protein Structures, Functions, and Interactions) || Integrating Prediction of Structure, Function, and Interactions

Bujnicki, Janusz M.

Year:

2008

Language:

english

File:

PDF, 670 KB

english, 2008

39

Structural and degradative aspects of ornithine decarboxylase antizyme inhibitor 2

Ramos-Molina, Bruno, Lambertos, Ana, Lopez-Contreras, Andrés J., Kasprzak, Joanna M., Czerwoniec, Anna, Bujnicki, Janusz M., Cremades, Asunción, Peñafiel, Rafael

Journal:

Year:

2014

Language:

english

File:

PDF, 2.70 MB

english, 2014

40

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

Bauer, Raphael André, Rother, Kristian, Moor, Peter, Reinert, Knut, Steinke, Thomas, Bujnicki, Janusz, Preissner, Robert

Journal:

Year:

2009

Language:

english

File:

PDF, 465 KB

english, 2009

41

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

42

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

43

A Dna Mimic Caught In The Act: 3D Electron Microscopy Shows Ecoki Methyltransferase In Complex With The T7 Antirestriction Protein Ocr.

Kennaway, Christopher, Obarska-Kosinska, Agnieszka, White, John H., Tuszynska, Irina, Cooper, Laurie P., Bujnicki, Janusz M., Trinick, John, Dryden, David T.F.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 34 KB

english, 2009

44

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

Izabela Sierocka,Lukasz P Kozlowski,Janusz M Bujnicki…

Journal:

BMC Plant Biology

Year:

2014

Language:

english

File:

PDF, 972 KB

english, 2014

45

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

Bheemanaik, Shivakumara, Bujnicki, Janusz M., Nagaraja, Valakunja, Rao, Desirazu N.

Journal:

Biological Chemistry

Year:

2006

Language:

english

File:

PDF, 364 KB

english, 2006

46

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

Budzko, Lucyna, Jackowiak, Paulina, Kamel, Karol, Sarzynska, Joanna, Bujnicki, Janusz M., Figlerowicz, Marek

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 5.13 MB

english, 2017

47

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

48

Is AID a monomer in solution?

Ashok S. Bhagwat, Michael A. Carpenter, Janusz M. Bujnicki

Journal:

Year:

2008

Language:

english

File:

PDF, 307 KB

english, 2008

49

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

Agnieszka Paziewska, Lucjan S. Wyrwicz, Janusz M. Bujnicki, Karol Bomsztyk, Jerzy Ostrowski

Journal:

Year:

2004

Language:

english

File:

PDF, 171 KB

english, 2004

50

Prediction of Protein Structures, Functions, and Interactions ||

Bujnicki, Janusz M.

Year:

2008

Language:

english

File:

PDF, 5.49 MB

english, 2008

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