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1

A QM-MD simulation approach to the analysis of FRET processes in (bio)molecular systems. A case study: complexes ofE. colipurine nucleoside phosphorylase and its mutants with formycin A

Sobieraj, M., Krzyśko, K. A., Jarmuła, A., Kalinowski, M. W., Lesyng, B., Prokopowicz, M., Cieśla, J., Gojdź, A., Kierdaszuk, B.

Journal:

Journal of Molecular Modeling

Year:

2015

Language:

english

File:

PDF, 1.95 MB

english, 2015

2

Different Activities of 5-Hydroxy-dUMP and 5-Hydroxymethyl-dUMP in Thymidylate Synthase-Catalyzed Reaction in View of Molecular Modeling and Structural Studies

Adam Jarmuła, Andrzej Leś, Wojciech Rode

Journal:

Bioorganic Chemistry

Year:

2000

Language:

english

File:

PDF, 168 KB

english, 2000

3

The aromaticity of 5,6-dihydroborauracil, borauracil and benzoborauracil systems

Tomasz Ruman, Adam Jarmuła, Wojciech Rode

Journal:

Bioorganic Chemistry

Year:

2010

Language:

english

File:

PDF, 227 KB

english, 2010

4

The effect of 5-substitution in the pyrimidine ring of dUMP on the interaction with thymidylate synthase: Molecular modeling and QSAR

Adam Jarmuła, Piotr Cieplak, Tadeusz M. Krygowski, Wojciech Rode

Journal:

Bioorganic & Medicinal Chemistry

Year:

2007

Language:

english

File:

PDF, 705 KB

english, 2007

5

Mechanism of influence of phosphorylation on serine 124 on a decrease of catalytic activity of human thymidylate synthase

Adam Jarmuła, Tomasz Frączyk, Piotr Cieplak, Wojciech Rode

Journal:

Bioorganic & Medicinal Chemistry

Year:

2010

Language:

english

File:

PDF, 1.83 MB

english, 2010

6

A molecular modeling study of the interaction of 2′-fluoro-substituted analogues of dUMP/FdUMP with thymidylate synthase

Adam Jarmuła, Anna Dowierciał, Wojciech Rode

Journal:

Bioorganic & Medicinal Chemistry Letters

Year:

2008

Language:

english

File:

PDF, 831 KB

english, 2008

7

5,10-Methylene-5,6,7,8-tetrahydrofolate conformational transitions upon binding to thymidylate synthase: molecular mechanics and continuum solvent studies

Adam Jarmuła, Piotr Cieplak, William R. Montfort

Journal:

Journal of Computer-Aided Molecular Design

Year:

2005

Language:

english

File:

PDF, 394 KB

english, 2005

8

X-ray Crystal andAb InitioStructures of 3′,5′-di-O-Acetyl-N(4)-Hydroxy-2′-Deoxycytidine and Its 5-Fluoro Analogue: Models of theN(4)-OH-dCMP andN(4)-OH-FdCMP Molecules Interacting with Thymidylate Synthase

Adam Jarmuła, Wojciech R. Rypniewski, Krzysztof Felczak, Wojciech Rode

Journal:

Structural Chemistry

Year:

2005

Language:

english

File:

PDF, 150 KB

english, 2005

9

The effect of the methoxy group on the geometry of the benzene ring supported by crystal structure studies and Ab Initio Calculations. Crystal and Molecular Structure of 4-(4-Methoxyphenyl)-2,6-diphenylpyridine and 1-Methyl-4-(4-methoxy-phenyl)-2,6-diphenylpyridinium perchlorate.

Tadcuzz Marek Krygowski, Romana Anulewicz, Adam Jarmula, Tomazz Ba̧k, Danuta Rasala, Sean Howard

Journal:

Year:

1994

Language:

english

File:

PDF, 608 KB

english, 1994

10

Relative free energies of binding to thymidylate synthase of 2- and/or 4-thio and/or 5-fluoro analogues of dUMP

Adam Jarmuła, Piotr Cieplak, Andrzej Leś, Wojciech Rode

Journal:

Journal of Computer-Aided Molecular Design

Year:

2003

Language:

english

File:

PDF, 299 KB

english, 2003

11

Synthesis and interactions with thymidylate synthase of 2,4-dithio analogues of BUMP and 5-fluoro-dUMP

Jolanta M. Dzik, Maria Bretner, Tadeusz Kulikowski, Barbara Gołos, Adam Jarmuła, Jarosław Poznański, Wojciech Rode, David Shugar

Journal:

Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology

Year:

1996

Language:

english

File:

PDF, 778 KB

english, 1996

12

Crystal structures of 5-fluoro-dUrd and its 2 and/or 4-thio analogues: models of substituted dUMP pyrimidine ring interacting with thymidylate synthase

Adam Jarmuła, Romana Anulewicz, Andrzej Leś, Michał K Cyrański, Ludwik Adamowicz, Maria Bretner, Krzysztof Felczak, Tadeusz Kulikowski, Tadeusz M Krygowski, Wojciech Rode

Journal:

Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology

Year:

1998

Language:

english

File:

PDF, 116 KB

english, 1998

13

Computational study of the effects of protein tyrosine nitrations on the catalytic activity of human thymidylate synthase

Jarmuła, Adam, Rode, Wojciech

Journal:

Journal of Computer-Aided Molecular Design

Year:

2013

Language:

english

File:

PDF, 1.37 MB

english, 2013

14

The β -sheet breakers and π-stacking

Jarmuła, Adam, Stępkowski, Dariusz

Journal:

Journal of Peptide Science

Year:

2013

Language:

english

File:

PDF, 1.16 MB

english, 2013

15

Crystal structure of phosphoramide-phosphorylated thymidylate synthase reveals pSer127, reflecting probably pHis to pSer phosphotransfer

Wilk, Piotr, Jarmuła, Adam, Ruman, Tomasz, Banaszak, Katarzyna, Rypniewski, Wojciech, Cieśla, Joanna, Dowierciał, Anna, Rode, Wojciech

Journal:

Bioorganic Chemistry

Year:

2014

Language:

english

File:

PDF, 1.30 MB

english, 2014

16

Crystal Structure of Mouse Thymidylate Synthase in Tertiary Complex with dUMP and Raltitrexed Reveals N-Terminus Architecture and Two Different Active Site Conformations

Dowierciał, Anna, Wilk, Piotr, Rypniewski, Wojciech, Rode, Wojciech, Jarmuła, Adam

Journal:

BioMed Research International

Year:

2014

Language:

english

File:

PDF, 6.27 MB

english, 2014

17

Hypothesis of a proton switch in QM/MM modelling of interaction of dUMP analogues with thymidylate synthase

Fusaro, Massimo, Jurkiewicz, Agata, Jarmuła, Adam, Leś, Andrzej, Rode, Wojciech

Journal:

Molecular Simulation

Year:

2010

Language:

english

File:

PDF, 645 KB

english, 2010

18

Properties of Phosphorylated Thymidylate Synthase

Frączyk, Tomasz, Ruman, Tomasz, Wilk, Piotr, Palmowski, Paweł, Rogowska-Wrzesinska, Adelina, Cieśla, Joanna, Zieliński, Zbigniew, Nizioł, Joanna, Jarmuła, Adam, Maj, Piotr, Gołos, Barbara, Wińska, Pat

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2015

Language:

english

File:

PDF, 1.01 MB

english, 2015

19

Phosphorylation of thymidylate synthase affects slow-binding inhibition by 5-fluoro-dUMP and N 4 -hydroxy-dCMP

Ludwiczak, Jan, Maj, Piotr, Wilk, Piotr, Frączyk, Tomasz, Ruman, Tomasz, Kierdaszuk, Borys, Jarmuła, Adam, Rode, Wojciech

Journal:

Molecular BioSystems

Year:

2016

Language:

english

File:

PDF, 2.03 MB

english, 2016

20

Human Dihydrofolate Reductase and Thymidylate Synthase form a complex in vitro and co-localize in normal and cancer cells

Antosiewicz, Anna, Jarmuła, Adam, Przybylska, Dorota, Mosieniak, Grażyna, Szczepanowska, Joanna, Kowalkowska, Anna, Rode, Wojciech, Cieśla, Joanna

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2016

Language:

english

File:

PDF, 2.04 MB

english, 2016

21

Crystal structures of complexes of mouse thymidylate synthase crystallized with N4-OH-dCMP alone or in the presence of N5,10-methylenetetrahydrofolate

Dowierciał, Anna, Jarmuła, Adam, Wilk, Piotr, Rypniewski, Wojciech, Kierdaszuk, Borys, Rode, Wojciech

Journal:

Year:

2013

Language:

english

File:

PDF, 973 KB

english, 2013

22

Overproduction in bacteria of mouse thymidylate synthase forms with point mutations in N4-hydroxy-dCMP binding site

Cieśla, Joanna, Mitkowski, Paweł, Gojdź, Adrian, Jarmuła, Adam, Rode, Wojciech

Journal:

New Biotechnology

Year:

2016

Language:

english

File:

PDF, 56 KB

english, 2016

23

Mouse thymidylate synthase does not show the inactive conformation, observed for the human enzyme

Dowierciał, Anna, Jarmuła, Adam, Wilk, Piotr, Rypniewski, Wojciech, Kowalska, Monika, Frączyk, Tomasz, Cieśla, Joanna, Rode, Wojciech

Journal:

Structural Chemistry

Year:

2017

Language:

english

File:

PDF, 2.55 MB

english, 2017

24

Crystal structures of thymidylate synthase from nematodes, Trichinella spiralis and Caenorhabditis elegans, as a potential template for species-specific drug design

Dowierciał, Anna, Wilk, Piotr, Rypniewski, Wojciech, Frączyk, Tomasz, Jarmuła, Adam, Banaszak, Katarzyna, Dąbrowska, Magdalena, Cieśla, Joanna, Rode, Wojciech

Journal:

Year:

2013

Language:

english

File:

PDF, 1.05 MB

english, 2013

25

APACHE II score predicts mortality in patients requiring prolonged ventilation in a weaning center

Rojek-Jarmuła, Anna, Hombach, Rainer, Krzych, Łukasz J.

Journal:

Anestezjologia Intensywna Terapia

Year:

2016

Language:

english

File:

PDF, 89 KB

english, 2016

26

APACHE II score cannot predict successful weaning from prolonged mechanical ventilation

Rojek-Jarmuła, Anna, Hombach, Rainer, Krzych, Łukasz J

Journal:

Chronic Respiratory Disease

Year:

2017

Language:

english

File:

PDF, 344 KB

english, 2017

27

[IEEE Conference on Electrical Insulation & Dielectric Phenomena - Annual Report 1981 - Whitehaven, PA, USA (1981.10.26-1981.10.28)] Conference on Electrical Insulation & Dielectric Phenomena - Annual Report 1981 - Laboratory testing of electrical insulating materials superficial resistance to HF vapours as selection criteria for SF6 circuit breakers insulators

Year:

1981

Language:

english

File:

PDF, 1.54 MB

english, 1981

28

Crystal structures of nematode (parasitic T. spiralis and free living C. elegans ), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics simulations in search for nematode-specific inhibitors of TS.

Jarmuła, Adam, Wilk, Piotr, Maj, Piotr, Ludwiczak, Jan, Dowierciał, Anna, Banaszak, Katarzyna, Rypniewski, Wojciech, Cieśla, Joanna, Dąbrowska, Magdalena, Frączyk, Tomasz, Bronowska, Agnieszka K., Jak

Journal:

Journal of Molecular Graphics and Modelling

Year:

2017

Language:

english

File:

PDF, 4.38 MB

english, 2017

29

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

30

Does the APACHE II score predict performance of activities of daily living in patients discharged from a weaning center?

Rojek-Jarmuła, Anna, Hombach, Rainer, Krzych, Łukasz J.

Journal:

Polish Journal of Cardio-Thoracic Surgery

Year:

2016

File:

PDF, 186 KB

2016

31

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

32

Interactions between motor domains in kinesin-14 Ncd - a molecular dynamics study

Ludwiczak, Jan, Szczęsna, Ewa, Marinho da Silva Neto, Antônio, Cieplak, Piotr, Kasprzak, Andrzej A, Jarmuła, Adam

Journal:

Biochemical Journal

Year:

2019

Language:

english

File:

PDF, 1.25 MB

english, 2019

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