BrIdging Structural BiOlogy with Biological SyNthesis and Self Assembly to Reveal Key Processes in Living Systems

Rezultaty

Annual report on strategic events Year 1

Programmes and attendance records

Annual report on strategic events Year 3

Programmes and attendance records

Management knowledge transfer report

Summary of staff exchange and workshop

Final report on expert visits

Programme and attendance records

Communication, dissemination, and exploitation plan

Indicative schedule and guidelines for dissemination, communication and exploitation

Mid-term training report

Summary of training events and student progress

Mid-term communication, dissemination, and exploitation report

Summary of activities, update of plan

Final secondment report

Summary of implemented secondments

Annual report on strategic events Year 2

Programmes and attendance records

Mid-term report on expert visits

Programme and attendance records

Training plan

Preliminary schedule of training events

List of CEITEC MU publications for the last 3 years

Key Performance Indicators (KPI) baseline. In the reporting tool on the Participant Portal by month 2 all publications of the coordinator (CEITEC MU in the particular field of research) during the three years preceding the start date of the BISON project will be added. The deliverable D7.1 will be one-page statement that this task has been completed.

Final training report

Summary of training events and student progress

Secondment plan

Preliminary secondment schedule and supervisory arrangements

Mid-term secondment report

Summary of implemented secondments and update of Secondment plan

Final communication, dissemination, and exploitation report

Summary of activities

Publikacje

Implementing efficient concerted rotations using Mathematica and C code⋆

Autorzy: Luca Tubiana, Miroslav Jurásek, Ivan Coluzza
Opublikowane w: The European Physical Journal E, Numer 41/7, 2018, ISSN 1292-8941
Wydawca: Springer Verlag
DOI: 10.1140/epje/i2018-11694-7

Functionally specific binding regions of microtubule-associated protein 2c exhibit distinct conformations and dynamics

Autorzy: Kateřina Melková, Vojtěch Zapletal, Séverine Jansen, Erik Nomilner, Milan Zachrdla, Jozef Hritz, Jiří Nováček, Markus Zweckstetter, Malene R. Jensen, Martin Blackledge, Lukáš Žídek
Opublikowane w: Journal of Biological Chemistry, Numer 293/34, 2018, Strona(/y) 13297-13309, ISSN 0021-9258
Wydawca: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.ra118.001769

Label-free Voltammetric Detection of Products of Terminal Deoxynucleotidyl Transferase Tailing Reaction

Autorzy: Monika Hermanová, Pavlína Havranová-Vidláková, Anna Ondráčková, Swathi Senthil Kumar, Richard Bowater, Miroslav Fojta
Opublikowane w: Electroanalysis, Numer 31/2, 2019, Strona(/y) 246-255, ISSN 1040-0397
Wydawca: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/elan.201800452

Asymmetric bifurcated halogen bonds

Autorzy: Martin Novák, Cina Foroutan-Nejad, Radek Marek
Opublikowane w: Phys. Chem. Chem. Phys., Numer 14639076, 2015, Strona(/y) 6440-6450, ISSN 1463-9076
Wydawca: Royal Society of Chemistry
DOI: 10.1039/c4cp05532b

DNA and RNA Quadruplex-Binding Proteins

Autorzy: Václav Brázda, Lucia Hároníková, Jack Liao, Miroslav Fojta
Opublikowane w: International Journal of Molecular Sciences, Numer 14220067, 2014, Strona(/y) 17493-17517, ISSN 1422-0067
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms151017493

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation

Autorzy: S. K. Mishra, M. Kara, M. Zacharias, J. Koca
Opublikowane w: Glycobiology, Numer 09596658, 2013, Strona(/y) 70-84, ISSN 0959-6658
Wydawca: Oxford University Press
DOI: 10.1093/glycob/cwt093

Electrochemical detection of DNA binding by tumor suppressor p53 protein using osmium-labeled oligonucleotide probes and catalytic hydrogen evolution at the mercury electrode

Autorzy: Kateřina Němcová, Peter Šebest, Luděk Havran, Petr Orság, Miroslav Fojta, Hana Pivoňková
Opublikowane w: Analytical and Bioanalytical Chemistry, Numer 16182642, 2014, Strona(/y) 5843-5852, ISSN 1618-2642
Wydawca: Springer Verlag
DOI: 10.1007/s00216-014-7996-0

Studying Weak and Dynamic Interactions of Posttranslationally Modified Proteins using Expressed Protein Ligation

Autorzy: Konstantinos Tripsianes, Nam K. Chu, Anders Friberg, Michael Sattler, Christian F. W. Becker
Opublikowane w: ACS Chemical Biology, Numer 15548929, 2014, Strona(/y) 347-352, ISSN 1554-8929
Wydawca: American Chemical Society
DOI: 10.1021/cb400723j

Spectral density mapping protocols for analysis of molecular motions in disordered proteins

Autorzy: Pavel Kadeřávek, Vojtěch Zapletal, Alžbeta Rabatinová, Libor Krásný, Vladimír Sklenář, Lukáš Žídek
Opublikowane w: Journal of Biomolecular NMR, Numer 09252738, 2014, Strona(/y) 193-207, ISSN 0925-2738
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s10858-014-9816-4

Vinylsulfonamide and Acrylamide Modification of DNA for Cross-linking with Proteins

Autorzy: Jitka Dadová, Petr Orság, Radek Pohl, Marie Brázdová, Miroslav Fojta, Michal Hocek
Opublikowane w: Angewandte Chemie International Edition, Numer 14337851, 2013, Strona(/y) 10515-10518, ISSN 1433-7851
Wydawca: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201303577

Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage ϕ6 Major Capsid Protein

Autorzy: Daniel Nemecek, Pavel Plevka, Evzen Boura
Opublikowane w: The Protein Journal, Numer 15723887, 2013, Strona(/y) 635-640, ISSN 1572-3887
Wydawca: Springer Verlag
DOI: 10.1007/s10930-013-9526-x

A relativistic DFT methodology for calculating the structures and NMR chemical shifts of octahedral platinum and iridium complexes

Autorzy: Jan Vícha, Michael Patzschke, Radek Marek
Opublikowane w: Physical Chemistry Chemical Physics, Numer 14639076, 2013, Strona(/y) 7740, ISSN 1463-9076
Wydawca: Royal Society of Chemistry
DOI: 10.1039/c3cp44440f

Voltammetric Study of dsDNA Modified by Multi-redox Label Based on N-methyl-4-hydrazino-7-nitrobenzofurazan

Autorzy: Ales Danhel, Veronika Raindlova, Ludek Havran, Jiri Barek, Michal Hocek, Miroslav Fojta
Opublikowane w: Electrochimica Acta, Numer 00134686, 2014, Strona(/y) 348-357, ISSN 0013-4686
Wydawca: Pergamon Press Ltd.
DOI: 10.1016/j.electacta.2014.02.137

Instability restricts signaling of multiple fibroblast growth factors

Autorzy: Marcela Buchtova, Radka Chaloupkova, Malgorzata Zakrzewska, Iva Vesela, Petra Cela, Jana Barathova, Iva Gudernova, Renata Zajickova, Lukas Trantirek, Jorge Martin, Michal Kostas, Jacek Otlewski, Jiri Damborsky, Alois Kozubik, Antoni Wiedlocha, Pavel Krejci
Opublikowane w: Cellular and Molecular Life Sciences, Numer 1420682X, 2015, Strona(/y) 2445-2459, ISSN 1420-682X
Wydawca: Birkhauser Verlag
DOI: 10.1007/s00018-015-1856-8

A Novel Protein-Protein Interaction in the RES (REtention and Splicing) Complex

Autorzy: K. Tripsianes, A. Friberg, C. Barrandon, M. Brooks, H. van Tilbeurgh, B. Seraphin, M. Sattler
Opublikowane w: Journal of Biological Chemistry, Numer 00219258, 2014, Strona(/y) 28640-28650, ISSN 0021-9258
Wydawca: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.M114.592311

How Ionic Strength Affects the Conformational Behavior of Human and Rat Beta Amyloids – A Computational Study

Autorzy: Zdeněk Kříž, Jiří Klusák, Zdena Krištofíková, Jaroslav Koča
Opublikowane w: PLoS ONE, Numer 19326203, 2013, Strona(/y) e62914, ISSN 1932-6203
Wydawca: Public Library of Science
DOI: 10.1371/journal.pone.0062914

Efficient protocol for backbone and side-chain assignments of large, intrinsically disordered proteins: transient secondary structure analysis of 49.2 kDa microtubule associated protein 2c

Autorzy: Jiří Nováček, Lubomír Janda, Radka Dopitová, Lukáš Žídek, Vladimír Sklenář
Opublikowane w: Journal of Biomolecular NMR, Numer 09252738, 2013, Strona(/y) 291-301, ISSN 0925-2738
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s10858-013-9761-7

Electrochemical behaviour of 2,4-dinitrophenylhydrazi(o)ne as multi-redox centre DNA label at mercury meniscus modified silver solid amalgam electrode

Autorzy: Ales Danhel, Veronika Raindlova, Ludek Havran, Hana Pivonkova, Michal Hocek, Miroslav Fojta
Opublikowane w: Electrochimica Acta, Numer 00134686, 2014, Strona(/y) 122-131, ISSN 0013-4686
Wydawca: Pergamon Press Ltd.
DOI: 10.1016/j.electacta.2013.09.147

High-quality and universal empirical atomic charges for chemoinformatics applications

Autorzy: Stanislav Geidl, Tomáš Bouchal, Tomáš Raček, Radka Svobodová Vařeková, Václav Hejret, Aleš Křenek, Ruben Abagyan, Jaroslav Koča
Opublikowane w: Journal of Cheminformatics, Numer 17582946, 2015, ISSN 1758-2946
Wydawca: Chemistry Central
DOI: 10.1186/s13321-015-0107-1

Potential energy surface and binding energy in the presence of an external electric field: modulation of anion–π interactions for graphene-based receptors

Autorzy: Cina Foroutan-Nejad, Radek Marek
Opublikowane w: Phys. Chem. Chem. Phys., Numer 14639076, 2014, Strona(/y) 2508-2514, ISSN 1463-9076
Wydawca: Royal Society of Chemistry
DOI: 10.1039/c3cp52671b

Electrochemistry of closo-dodecaborate dianion and its simple exo-skeletal derivatives at carbon electrodes in aqueous phosphate buffers

Autorzy: Lukáš Fojt, Miroslav Fojta, Bohumír Grüner, Radim Vespalec
Opublikowane w: Journal of Electroanalytical Chemistry, Numer 15726657, 2013, Strona(/y) 38-42, ISSN 1572-6657
Wydawca: Elsevier BV
DOI: 10.1016/j.jelechem.2013.08.016

Multiple Recognition Motifs in Nucleoporin Nup159 Provide a Stable and Rigid Nup159-Dyn2 Assembly

Autorzy: A. Nyarko, Y. Song, J. Novacek, L. Zidek, E. Barbar
Opublikowane w: Journal of Biological Chemistry, Numer 00219258, 2013, Strona(/y) 2614-2622, ISSN 0021-9258
Wydawca: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.M112.432831

Diverse effects of naturally occurring base lesions on the structure and stability of the human telomere DNA quadruplex

Autorzy: Helena Konvalinová, Zuzana Dvořáková, Daniel Renčiuk, Klára Bednářová, Iva Kejnovská, Lukáš Trantírek, Michaela Vorlíčková, Janos Sagi
Opublikowane w: Biochimie, Numer 03009084, 2015, Strona(/y) 15-25, ISSN 0300-9084
Wydawca: Elsevier BV
DOI: 10.1016/j.biochi.2015.07.013

Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands

Autorzy: Sophia Bazzi, Jan Novotný, Yevgen P. Yurenko, Radek Marek
Opublikowane w: Chemistry - A European Journal, Numer 09476539, 2015, Strona(/y) 9414-9425, ISSN 0947-6539
Wydawca: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201500743

Expression of FGF19 in human embryonic stem cells

Autorzy: Pavel Krejci, Michaela Kunova, Iva Kubikova, Lukas Trantirek, Alois Kozubik, Petr Dvorak
Opublikowane w: STEM CELLS, Numer 10665099, 2013, Strona(/y) 2582-2584, ISSN 1066-5099
Wydawca: AlphaMed Press Inc
DOI: 10.1002/stem.1493

Electrochemical behavior of anthraquinone- and nitrophenyl-labeled deoxynucleoside triphosphates: a contribution to development of multipotential redox labeling of DNA

Autorzy: Pavlína Vidláková, Hana Pivoňková, Miroslav Fojta, Luděk Havran
Opublikowane w: Monatshefte für Chemie - Chemical Monthly, Numer 00269247, 2015, Strona(/y) 839-847, ISSN 0026-9247
Wydawca: Springer Verlag
DOI: 10.1007/s00706-015-1435-6

Biophysical and electrochemical studies of protein–nucleic acid interactions

Autorzy: Richard P. Bowater, Andrew M. Cobb, Hana Pivonkova, Ludek Havran, Miroslav Fojta
Opublikowane w: Monatshefte für Chemie - Chemical Monthly, Numer 00269247, 2015, Strona(/y) 723-739, ISSN 0026-9247
Wydawca: Springer Verlag
DOI: 10.1007/s00706-014-1405-4

Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2

Autorzy: Tomáš Trnka, Stanislav Kozmon, Igor Tvaroška, Jaroslav Koča
Opublikowane w: PLOS Computational Biology, Numer 1553734X, 2015, Strona(/y) e1004061, ISSN 1553-734X
Wydawca: Public Library of Science
DOI: 10.1371/journal.pcbi.1004061

Understanding the Electronic Factors Responsible for Ligand Spin–Orbit NMR Shielding in Transition-Metal Complexes

Autorzy: Jan Vícha, Cina Foroutan-Nejad, Tomasz Pawlak, Markéta L. Munzarová, Michal Straka, Radek Marek
Opublikowane w: Journal of Chemical Theory and Computation, Numer 15499618, 2015, Strona(/y) 1509-1517, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/ct501089z

Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic 15N chemical shielding anisotropy tensors

Autorzy: Jiří Emmer, Andrea Vavrinská, Vladimír Sychrovský, Ladislav Benda, Zdeněk Kříž, Jaroslav Koča, Rolf Boelens, Vladimír Sklenář, Lukáš Trantírek
Opublikowane w: Journal of Biomolecular NMR, Numer 09252738, 2013, Strona(/y) 59-70, ISSN 0925-2738
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s10858-012-9686-6

Differential Salt-Induced Dissociation of the p53 Protein Complexes with Circular and Linear Plasmid DNA Substrates Suggest Involvement of a Sliding Mechanism

Autorzy: Peter Šebest, Marie Brázdová, Miroslav Fojta, Hana Pivoňková
Opublikowane w: International Journal of Molecular Sciences, Numer 14220067, 2015, Strona(/y) 3163-3177, ISSN 1422-0067
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms16023163

Polymerase synthesis of oligonucleotides containing a single chemically modified nucleobase for site-specific redox labelling

Autorzy: Petra Ménová, Hana Cahová, Medard Plucnara, Luděk Havran, Miroslav Fojta, Michal Hocek
Opublikowane w: Chemical Communications, Numer 13597345, 2013, Strona(/y) 4652, ISSN 1359-7345
Wydawca: Royal Society of Chemistry
DOI: 10.1039/c3cc41438h

A novel variant of FGFR3 causes proportionate short stature

Autorzy: S. G. Kant, I. Cervenkova, L. Balek, L. Trantirek, G. W. E. Santen, M. C. de Vries, H. A. van Duyvenvoorde, M. J. R. van der Wielen, A. J. M. H. Verkerk, A. G. Uitterlinden, S. E. Hannema, J. M. Wit, W. Oostdijk, P. Krejci, M. Losekoot
Opublikowane w: European Journal of Endocrinology, Numer 08044643, 2015, Strona(/y) 763-770, ISSN 0804-4643
Wydawca: BioScientifica Ltd.
DOI: 10.1530/EJE-14-0945

In-Cell NMR and EPR Spectroscopy of Biomacromolecules

Autorzy: Robert Hänsel, Laura M. Luh, Ivan Corbeski, Lukáš Trantirek, Volker Dötsch
Opublikowane w: Angewandte Chemie International Edition, Numer 14337851, 2014, Strona(/y) 10300-10314, ISSN 1433-7851
Wydawca: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201311320

Aqueous Heck Cross-Coupling Preparation of Acrylate-Modified Nucleotides and Nucleoside Triphosphates for Polymerase Synthesis of Acrylate-Labeled DNA

Autorzy: Jitka Dadová, Pavlína Vidláková, Radek Pohl, Luděk Havran, Miroslav Fojta, Michal Hocek
Opublikowane w: The Journal of Organic Chemistry, Numer 00223263, 2013, Strona(/y) 9627-9637, ISSN 0022-3263
Wydawca: American Chemical Society
DOI: 10.1021/jo4011574

Molecular Basis for Coordinating Transcription Termination with Noncoding RNA Degradation

Autorzy: Agnieszka Tudek, Odil Porrua, Tomasz Kabzinski, Michael Lidschreiber, Karel Kubicek, Andrea Fortova, François Lacroute, Stepanka Vanacova, Patrick Cramer, Richard Stefl, Domenico Libri
Opublikowane w: Molecular Cell, Numer 10972765, 2014, Strona(/y) 467-481, ISSN 1097-2765
Wydawca: Cell Press
DOI: 10.1016/j.molcel.2014.05.031

Exploring Reaction Pathways for O -GlcNAc Transferase Catalysis. A String Method Study

Autorzy: Manju Kumari, Stanislav Kozmon, Petr Kulhánek, Jakub Štepán, Igor Tvaroška, Jaroslav Koča
Opublikowane w: The Journal of Physical Chemistry B, Numer 15206106, 2015, Strona(/y) 4371-4381, ISSN 1520-6106
Wydawca: American Chemical Society
DOI: 10.1021/jp511235f

Autorzy: Pavel Kadeřávek, Sarina Grutsch, Nicola Salvi, Martin Tollinger, Lukáš Žídek, Geoffrey Bodenhausen, Fabien Ferrage
Opublikowane w: Journal of Biomolecular NMR, Numer 09252738, 2015, Strona(/y) 353-365, ISSN 0925-2738
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s10858-015-9994-8

Structural Study of the Partially Disordered Full-Length δ Subunit of RNA Polymerase from Bacillus subtilis

Autorzy: Veronika Papoušková, Pavel Kadeřávek, Olga Otrusinová, Alžbeta Rabatinová, Hana Šanderová, Jiří Nováček, Libor Krásný, Vladimír Sklenář, Lukáš Žídek
Opublikowane w: ChemBioChem, Numer 14394227, 2013, Strona(/y) 1772-1779, ISSN 1439-4227
Wydawca: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.201300226

Origin of the Conformational Modulation of the 13 C NMR Chemical Shift of Methoxy Groups in Aromatic Natural Compounds

Autorzy: Jaromír Toušek, Michal Straka, Vladimír Sklenář, Radek Marek
Opublikowane w: The Journal of Physical Chemistry A, Numer 10895639, 2013, Strona(/y) 661-669, ISSN 1089-5639
Wydawca: American Chemical Society
DOI: 10.1021/jp310470f

High-Resolution Insight into G-Overhang Architecture

Autorzy: Robert Hänsel, Frank Löhr, Lukáš Trantirek, Volker Dötsch
Opublikowane w: Journal of the American Chemical Society, Numer 00027863, 2013, Strona(/y) 2816-2824, ISSN 0002-7863
Wydawca: American Chemical Society
DOI: 10.1021/ja312403b

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes

Autorzy: R. S. Va ekova, D. Jaiswal, D. Sehnal, C.-M. Ionescu, S. Geidl, L. Pravda, V. Horsky, M. Wimmerova, J. Ko a
Opublikowane w: Nucleic Acids Research, Numer 03051048, 2014, Strona(/y) W227-W233, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gku426

Structural insights into Aspergillus fumigatus lectin specificity: AFL binding sites are functionally non-equivalent

Autorzy: Josef Houser, Jan Komarek, Gianluca Cioci, Annabelle Varrot, Anne Imberty, Michaela Wimmerova
Opublikowane w: Acta Crystallographica Section D Biological Crystallography, Numer 13990047, 2015, Strona(/y) 442-453, ISSN 1399-0047
Wydawca: Wiley-Blackwell
DOI: 10.1107/S1399004714026595

The Subunit of RNA Polymerase Is Required for Rapid Changes in Gene Expression and Competitive Fitness of the Cell

Autorzy: A. Rabatinova, H. Sanderova, J. Jirat Matejckova, J. Korelusova, L. Sojka, I. Barvik, V. Papouskova, V. Sklenar, L. Zidek, L. Krasny
Opublikowane w: Journal of Bacteriology, Numer 00219193, 2013, Strona(/y) 2603-2611, ISSN 0021-9193
Wydawca: American Society for Microbiology
DOI: 10.1128/JB.00188-13

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

Autorzy: Petr Stadlbauer, Petra Kührová, Pavel Banáš, Jaroslav Koča, Giovanni Bussi, Lukáš Trantírek, Michal Otyepka, Jiří Šponer
Opublikowane w: Nucleic Acids Research, Numer 03051048, 2015, Strona(/y) gkv994, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkv994

Extended molecular dynamics of a c-kit promoter quadruplex

Autorzy: Barira Islam, Petr Stadlbauer, Miroslav Krepl, Jaroslav Koca, Stephen Neidle, Shozeb Haider, Jiri Sponer
Opublikowane w: Nucleic Acids Research, Numer 03051048, 2015, Strona(/y) 8673-8693, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkv785

New sensitive detection method for lectin hemagglutination using microscopy

Autorzy: Lenka Adamová, Lenka Malinovská, Michaela Wimmerová
Opublikowane w: Microscopy Research and Technique, Numer 1059910X, 2014, Strona(/y) 841-849, ISSN 1059-910X
Wydawca: John Wiley & Sons Inc.
DOI: 10.1002/jemt.22407

Mammalian DIS3L2 exoribonuclease targets the uridylated precursors of let-7 miRNAs

Autorzy: D. Ustianenko, D. Hrossova, D. Potesil, K. Chalupnikova, K. Hrazdilova, J. Pachernik, K. Cetkovska, S. Uldrijan, Z. Zdrahal, S. Vanacova
Opublikowane w: RNA, Numer 13558382, 2013, Strona(/y) 1632-1638, ISSN 1355-8382
Wydawca: Cold Spring Harbor Laboratory Press
DOI: 10.1261/rna.040055.113

Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity

Autorzy: Zdeněk Kříž, Jan Adam, Jana Mrázková, Petros Zotos, Thomais Chatzipavlou, Michaela Wimmerová, Jaroslav Koča
Opublikowane w: Journal of Computer-Aided Molecular Design, Numer 0920654X, 2014, Strona(/y) 951-960, ISSN 0920-654X
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s10822-014-9774-7

Structure and NMR properties of 6-substituted-5,6-dihydrobenzo[ c ]phenanthridine alkaloids

Autorzy: Shivaji S. Kadam, Lukáš Maier, Tomáš Šolomek, Marek Nečas, Karel Šmejkal, Jiří Dostál, Vladimír Sklenář, Radek Marek
Opublikowane w: Journal of Physical Organic Chemistry, Numer 08943230, 2013, Strona(/y) 814-821, ISSN 0894-3230
Wydawca: John Wiley & Sons Inc.
DOI: 10.1002/poc.3175

Conformational Dynamics and Antigenicity in the Disordered Malaria Antigen Merozoite Surface Protein 2

Autorzy: Christopher A. MacRaild, Milan Zachrdla, Dean Andrew, Bankala Krishnarjuna, Jiří Nováček, Lukáš Žídek, Vladimír Sklenář, Jack S. Richards, James G. Beeson, Robin F. Anders, Raymond S. Norton
Opublikowane w: PLOS ONE, Numer 19326203, 2015, Strona(/y) e0119899, ISSN 1932-6203
Wydawca: Public Library of Science
DOI: 10.1371/journal.pone.0119899

Preferential Binding of Hot Spot Mutant p53 Proteins to Supercoiled DNA In Vitro and in Cells

Autorzy: Marie Brázdová, Lucie Navrátilová, Vlastimil Tichý, Kateřina Němcová, Matej Lexa, Roman Hrstka, Petr Pečinka, Matej Adámik, Borivoj Vojtesek, Emil Paleček, Wolfgang Deppert, Miroslav Fojta
Opublikowane w: PLoS ONE, Numer 19326203, 2013, Strona(/y) e59567, ISSN 1932-6203
Wydawca: Public Library of Science
DOI: 10.1371/journal.pone.0059567

How Does the Methodology of 3D Structure Preparation Influence the Quality of p K a Prediction?

Autorzy: Stanislav Geidl, Radka Svobodová Vařeková, Veronika Bendová, Lukáš Petrusek, Crina-Maria Ionescu, Zdeněk Jurka, Ruben Abagyan, Jaroslav Koča
Opublikowane w: Journal of Chemical Information and Modeling, Numer 15499596, 2015, Strona(/y) 1088-1097, ISSN 1549-9596
Wydawca: American Chemical Society
DOI: 10.1021/ci500758w

Azidopropylvinylsulfonamide as a New Bifunctional Click Reagent for Bioorthogonal Conjugations: Application for DNA-Protein Cross-Linking

Autorzy: Jitka Dadová, Milan Vrábel, Matej Adámik, Marie Brázdová, Radek Pohl, Miroslav Fojta, Michal Hocek
Opublikowane w: Chemistry - A European Journal, Numer 09476539, 2015, Strona(/y) 16091-16102, ISSN 0947-6539
Wydawca: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201502209

A QM/MM Investigation of the Catalytic Mechanism of Metal-Ion-Independent Core 2 β1,6- N -Acetylglucosaminyltransferase

Autorzy: Igor Tvaroška, Stanislav Kozmon, Michaela Wimmerová, Jaroslav Koča
Opublikowane w: Chemistry - A European Journal, Numer 09476539, 2013, Strona(/y) 8153-8162, ISSN 0947-6539
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Design of Stereoelectronically Promoted Super Lewis Acids and Unprecedented Chemistry of Their Complexes

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Opublikowane w: Chemistry - A European Journal, Numer 09476539, 2014, Strona(/y) 11584-11590, ISSN 0947-6539
Wydawca: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201402582

Substituting CF 2 for O4′ in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions

Autorzy: Yevgen P. Yurenko, Jan Novotný, Vladimir Sklenář, Radek Marek
Opublikowane w: Chemistry - A European Journal, Numer 09476539, 2015, Strona(/y) 17933-17943, ISSN 0947-6539
Wydawca: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201502977

Catalytic oxidation of aromatic hydrocarbons by mono-oxido-alkoxidovanadium(V) complexes of ONNO donor ethylenediamine-bis(phenolate) ligands

Autorzy: Mainak Debnath, Arpan Dutta, Surajit Biswas, Kalyan Kumar Das, Hon Man Lee, Jan Vícha, Radek Marek, Jaromir Marek, Mahammad Ali
Opublikowane w: Polyhedron, Numer 02775387, 2013, Strona(/y) 189-198, ISSN 0277-5387
Wydawca: Pergamon Press
DOI: 10.1016/j.poly.2013.07.013

Targeted In Vivo Inhibition of Specific Protein–Protein Interactions Using Recombinant Antibodies

Autorzy: Matej Zábrady, Vendula Hrdinová, Bruno Müller, Udo Conrad, Jan Hejátko, Lubomír Janda
Opublikowane w: PLoS ONE, Numer 19326203, 2014, Strona(/y) e109875, ISSN 1932-6203
Wydawca: Public Library of Science
DOI: 10.1371/journal.pone.0109875

Predicting p Ka values from EEM atomic charges

Autorzy: Radka Vařeková, Stanislav Geidl, Crina-Maria Ionescu, Ondřej Skřehota, Tomáš Bouchal, David Sehnal, Ruben Abagyan, Jaroslav Koča
Opublikowane w: Journal of Cheminformatics, Numer 17582946, 2013, Strona(/y) 18, ISSN 1758-2946
Wydawca: Chemistry Central
DOI: 10.1186/1758-2946-5-18

On the non-classical contribution in lone-pair–π interaction: IQA perspective

Autorzy: Zahra Badri, Cina Foroutan-Nejad, Jiri Kozelka, Radek Marek
Opublikowane w: Phys. Chem. Chem. Phys., Numer 14639076, 2015, Strona(/y) 26183-26190, ISSN 1463-9076
Wydawca: Royal Society of Chemistry
DOI: 10.1039/c5cp04489h

Enzyme-linked electrochemical DNA ligation assay using magnetic beads

Autorzy: Eva Stejskalová, Petra Horáková, Jan Vacek, Richard P. Bowater, Miroslav Fojta
Opublikowane w: Analytical and Bioanalytical Chemistry, Numer 16182642, 2014, Strona(/y) 4129-4136, ISSN 1618-2642
Wydawca: Springer Verlag
DOI: 10.1007/s00216-014-7811-y

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