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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

Mechanism of Regulation of Receptor Histidine Kinases

Hedda U. Ferris, Stanislaw Dunin-Horkawicz, Nora Hornig, Michael Hulko, Jörg Martin, Joachim E. Schultz, Kornelius Zeth, Andrei N. Lupas, Murray Coles

Journal:

Year:

2012

Language:

english

File:

PDF, 1.64 MB

english, 2012

3

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

4

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

5

The GD box: A widespread noncontiguous supersecondary structural element

Vikram Alva, Stanislaw Dunin-Horkawicz, Michael Habeck, Murray Coles, Andrei N. Lupas

Journal:

Protein Science

Year:

2009

Language:

english

File:

PDF, 426 KB

english, 2009

6

The Mechanisms of HAMP-Mediated Signaling in Transmembrane Receptors

Hedda U. Ferris, Stanislaw Dunin-Horkawicz, Laura García Mondéjar, Michael Hulko, Klaus Hantke, Jörg Martin, Joachim E. Schultz, Kornelius Zeth, Andrei N. Lupas, Murray Coles

Journal:

Year:

2011

Language:

english

File:

PDF, 1.01 MB

english, 2011

7

Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases

Karolina L Tkaczuk, Stanislaw Dunin-Horkawicz, Elzbieta Purta, Janusz M Bujnicki

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 5.14 MB

english, 2007

8

Phylogenomic analysis of the GIY-YIG nuclease superfamily

Stanislaw Dunin-Horkawicz, Marcin Feder, Janusz M Bujnicki

Journal:

Year:

2006

Language:

english

File:

PDF, 3.56 MB

english, 2006

9

Comprehensive Analysis of HAMP Domains: Implications for Transmembrane Signal Transduction

Stanislaw Dunin-Horkawicz, Andrei N. Lupas

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 7.79 MB

english, 2010

10

A transition from strong right-handed to canonical left-handed supercoiling in a conserved coiled-coil segment of trimeric autotransporter adhesins

Birte Hernandez Alvarez, Markus Gruber, Astrid Ursinus, Stanislaw Dunin-Horkawicz, Andrei N. Lupas, Kornelius Zeth

Journal:

Journal of Structural Biology

Year:

2010

Language:

english

File:

PDF, 1.79 MB

english, 2010

11

Measuring the conformational space of square four-helical bundles with the program samCC

Stanislaw Dunin-Horkawicz, Andrei N. Lupas

Journal:

Journal of Structural Biology

Year:

2010

Language:

english

File:

PDF, 1010 KB

english, 2010

12

Complete fiber structures of complex trimeric autotransporter adhesins conserved in enterobacteria

Hartmann, M. D., Grin, I., Dunin-Horkawicz, S., Deiss, S., Linke, D., Lupas, A. N., Hernandez Alvarez, B.

Journal:

Proceedings of the National Academy of Sciences

Year:

2012

Language:

english

File:

PDF, 1.55 MB

english, 2012

13

Rational Design of Helical Nanotubes from Self-Assembly of Coiled-Coil Lock Washers

Xu, Chunfu, Liu, Rui, Mehta, Anil K., Guerrero-Ferreira, Ricardo C., Wright, Elizabeth R., Dunin-Horkawicz, Stanislaw, Morris, Kyle, Serpell, Louise C., Zuo, Xiaobing, Wall, Joseph S., Conticello, Vin

Journal:

Journal of the American Chemical Society

Year:

2013

Language:

english

File:

PDF, 1.77 MB

english, 2013

14

Computational modeling of protein–RNA complex structures

Tuszynska, Irina, Matelska, Dorota, Magnus, Marcin, Chojnowski, Grzegorz, Kasprzak, Joanna M., Kozlowski, Lukasz P., Dunin-Horkawicz, Stanislaw, Bujnicki, Janusz M.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.34 MB

english, 2014

15

A soluble mutant of the transmembrane receptor Af1503 features strong changes in coiled-coil periodicity

Hartmann, Marcus D., Dunin-Horkawicz, Stanislaw, Hulko, Michael, Martin, Jörg, Coles, Murray, Lupas, Andrei N.

Journal:

Journal of Structural Biology

Year:

2014

Language:

english

File:

PDF, 2.87 MB

english, 2014

16

Axial helix rotation as a mechanism for signal regulation inferred from the crystallographic analysis of the E. coli serine chemoreceptor

Ferris, Hedda U., Zeth, Kornelius, Hulko, Michael, Dunin-Horkawicz, Stanislaw, Lupas, Andrei N.

Journal:

Journal of Structural Biology

Year:

2014

Language:

english

File:

PDF, 1.58 MB

english, 2014

17

Prokaryotic Ancestry of Eukaryotic Protein Networks Mediating Innate Immunity and Apoptosis

Dunin-Horkawicz, Stanislaw, Kopec, Klaus O., Lupas, Andrei N.

Journal:

Journal of Molecular Biology

Year:

2014

Language:

english

File:

PDF, 2.51 MB

english, 2014

18

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

Szczepaniak, Krzysztof, Lach, Grzegorz, Bujnicki, Janusz M., Dunin-Horkawicz, Stanislaw

Journal:

Journal of Structural Biology

Year:

2014

Language:

english

File:

PDF, 2.94 MB

english, 2014

19

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

Matelska, D., Purta, E., Panek, S., Boniecki, M. J., Bujnicki, J. M., Dunin-Horkawicz, S.

Journal:

Year:

2013

Language:

english

File:

PDF, 621 KB

english, 2013

20

Self-Inflicted Eye Injuries*

Segal, Pawel, Mrzyglod, Stanislaw, Alichniewicz-Czaplicka, Halina, Dunin-Horkawicz, Wiktor, Zwyrzykowski, Eugeniusz

Journal:

American Journal of Ophthalmology

Year:

1963

Language:

english

File:

PDF, 6.37 MB

english, 1963

21

MODOMICS: a database of RNA modification pathways

Dunin-Horkawicz, S.

Journal:

Nucleic Acids Research

Year:

2006

Language:

english

File:

PDF, 1.05 MB

english, 2006

22

A coiled-coil motif that sequesters ions to the hydrophobic core

Hartmann, M. D., Ridderbusch, O., Zeth, K., Albrecht, R., Testa, O., Woolfson, D. N., Sauer, G., Dunin-Horkawicz, S., Lupas, A. N., Alvarez, B. H.

Journal:

Proceedings of the National Academy of Sciences

Year:

2009

Language:

english

File:

PDF, 1.74 MB

english, 2009

23

Novel Highly Thermostable Endolysin from Thermus scotoductus MAT2119 Bacteriophage Ph2119 with Amino Acid Sequence Similarity to Eukaryotic Peptidoglycan Recognition Proteins

Plotka, M., Kaczorowska, A.-K., Stefanska, A., Morzywolek, A., Fridjonsson, O. H., Dunin-Horkawicz, S., Kozlowski, L., Hreggvidsson, G. O., Kristjansson, J. K., Dabrowski, S., Bujnicki, J. M., Kaczoro

Journal:

Applied and Environmental Microbiology

Year:

2014

Language:

english

File:

PDF, 1.90 MB

english, 2014

24

MODOMICS: a database of RNA modification pathways. 2008 update

Czerwoniec, A., Dunin-Horkawicz, S., Purta, E., Kaminska, K. H., Kasprzak, J. M., Bujnicki, J. M., Grosjean, H., Rother, K.

Journal:

Nucleic Acids Research

Year:

2009

Language:

english

File:

PDF, 3.74 MB

english, 2009

25

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

Machnicka, M. A., Milanowska, K., Osman Oglou, O., Purta, E., Kurkowska, M., Olchowik, A., Januszewski, W., Kalinowski, S., Dunin-Horkawicz, S., Rother, K. M., Helm, M., Bujnicki, J. M., Grosjean, H.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.10 MB

english, 2013

26

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

Poleszak, K., Kaminska, K. H., Dunin-Horkawicz, S., Lupas, A., Skowronek, K. J., Bujnicki, J. M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 7.34 MB

english, 2012

27

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

Majorek, K. A., Dunin-Horkawicz, S., Steczkiewicz, K., Muszewska, A., Nowotny, M., Ginalski, K., Bujnicki, J. M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 12.98 MB

english, 2014

28

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

Blatter, Markus, Dunin-Horkawicz, Stanislaw, Grishina, Inna, Maris, Christophe, Thore, Stephane, Maier, Timm, Bindereif, Albrecht, Bujnicki, Janusz M., Allain, Frédéric H.-T.

Journal:

Journal of Molecular Biology

Year:

2015

Language:

english

File:

PDF, 2.90 MB

english, 2015

29

STAC—A New Domain Associated with Transmembrane Solute Transport and Two-Component Signal Transduction Systems

Korycinski, Mateusz, Albrecht, Reinhard, Ursinus, Astrid, Hartmann, Marcus D., Coles, Murray, Martin, Jörg, Dunin-Horkawicz, Stanislaw, Lupas, Andrei N.

Journal:

Journal of Molecular Biology

Year:

2015

Language:

english

File:

PDF, 2.05 MB

english, 2015

30

Loss of conserved non-coding RNAs in genomes of bacterial endosymbionts

Matelska, Dorota, Kurkowska, Malgorzata, Purta, Elzbieta, Bujnicki, Janusz M., Dunin-Horkawicz, Stanislaw

Journal:

Genome Biology and Evolution

Year:

2016

Language:

english

File:

PDF, 3.15 MB

english, 2016

31

Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori

Yahara, Koji, Furuta, Yoshikazu, Morimoto, Shinpei, Kikutake, Chie, Komukai, Sho, Matelska, Dorota, Dunin-Horkawicz, Stanisław, Bujnicki, Janusz M., Uchiyama, Ikuo, Kobayashi, Ichizo

Journal:

Year:

2016

Language:

english

File:

PDF, 544 KB

english, 2016

32

tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs

Machnicka, Magdalena A., Dunin-Horkawicz, Stanislaw, de Crécy-Lagard, Valérie, Bujnicki, Janusz M.

Journal:

Year:

2016

Language:

english

File:

PDF, 2.18 MB

english, 2016

33

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

Machnicka, Magdalena A., Kaminska, Katarzyna H., Dunin-Horkawicz, Stanislaw, Bujnicki, Janusz M.

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 6.46 MB

english, 2015

34

Two unique membrane-bound AAA proteins from Sulfolobus solfataricus

Serek-Heuberger, Justyna, Hobel, Cédric F.V., Dunin-Horkawicz, Stanislaw, Rockel, Beate, Martin, Jörg, Lupas, Andrei N.

Journal:

Biochemical Society Transactions

Year:

2009

Language:

english

File:

PDF, 788 KB

english, 2009

35

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

Boccaletto, Pietro, Magnus, Marcin, Almeida, Catarina, Żyła, Adriana, Astha, Astha, Pluta, Radosław, Bagiński, Błażej, Jankowska, Elżbieta, Dunin-Horkawicz, Stanisław, Wirecki, Tomasz K., Boniecki, Mi

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 816 KB

english, 2017

36

Combining Rosetta with molecular dynamics (MD): a benchmark of the MD-based ensemble protein design

Ludwiczak, Jan, Jarmula, Adam, Dunin-Horkawicz, Stanislaw

Journal:

Journal of Structural Biology

Year:

2018

Language:

english

File:

PDF, 1.32 MB

english, 2018

37

Variability of the core geometry in parallel coiled-coil bundles

Szczepaniak, Krzysztof, Ludwiczak, Jan, Winski, Aleksander, Dunin-Horkawicz, Stanislaw

Journal:

Journal of Structural Biology

Year:

2018

Language:

english

File:

PDF, 2.06 MB

english, 2018

38

Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain

Bocian-Ostrzycka, Katarzyna M., Łasica, Anna M., Dunin-Horkawicz, Stanisław, Grzeszczuk, Magdalena J., Drabik, Karolina, Dobosz, Aneta M., Godlewska, Renata, Nowak, Elżbieta, Collet, Jean-Francois, Ja

Journal:

Frontiers in Microbiology

Year:

2015

Language:

english

File:

PDF, 3.19 MB

english, 2015

39

Impact of selected amino acids of HP0377 (Helicobacter pylori thiol oxidoreductase) on its functioning as a CcmG (cytochrome c maturation) protein and Dsb (disulfide bond) isomerase

Grzeszczuk, Magdalena Joanna, Bąk, Aleksandra, Banaś, Anna Marta, Urbanowicz, Paweł, Dunin-Horkawicz, Stanislaw, Gieldon, Artur, Czaplewski, Cezary, Liwo, Adam, Jagusztyn-Krynicka, Elżbieta K., Franco

Journal:

Year:

2018

Language:

english

File:

PDF, 20.70 MB

english, 2018

40

DeepCoil – a fast and accurate prediction of coiled-coil domains in protein sequences

Ludwiczak, Jan, Winski, Aleksander, Szczepaniak, Krzysztof, Alva, Vikram, Dunin-Horkawicz, Stanislaw, Hancock, John

Journal:

Year:

2019

Language:

english

File:

PDF, 389 KB

english, 2019

41

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

File:

PDF, 1.91 MB

2019

42

ANO5 mutations in the Polish limb girdle muscular dystrophy patients: Effects on the protein structure

Jarmula, Adam, Łusakowska, Anna, Fichna, Jakub P., Topolewska, Malgorzata, Macias, Anna, Johnson, Katherine, Töpf, Ana, Straub, Volker, Rosiak, Edyta, Szczepaniak, Krzysztof, Dunin-Horkawicz, Stanisła

Journal:

Scientific Reports

Year:

2019

Language:

english

File:

PDF, 3.47 MB

english, 2019

43

C8J_1298, a bifunctional thiol oxidoreductase of Campylobacter jejuni, affects Dsb (disulfide bond) network functioning

BanaÅ, Anna Marta, Bocian-Ostrzycka, Katarzyna Marta, Plichta, Maciej, Dunin-Horkawicz, StanisÅaw, Ludwiczak, Jan, PÅaczkiewicz, Jagoda, Jagusztyn-Krynicka, ElÅ¼bieta Katarzyna, Franco, Rodrigo

Journal:

Year:

2020

File:

PDF, 3.97 MB

2020

44

Self-analysis of repeat proteins reveals evolutionarily conserved patterns

Merski, Matthew, MÅynarczyk, Krzysztof, Ludwiczak, Jan, Skrzeczkowski, Jakub, Dunin-Horkawicz, StanisÅaw, GÃ³rna, Maria W.

Journal:

BMC Bioinformatics

Year:

2020

File:

PDF, 1.29 MB

2020