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

Resultado final

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

Publicaciones

Implementing efficient concerted rotations using Mathematica and C code⋆

Autores: Luca Tubiana, Miroslav Jurásek, Ivan Coluzza
Publicado en: The European Physical Journal E, Edición 41/7, 2018, ISSN 1292-8941
Editor: Springer Verlag
DOI: 10.1140/epje/i2018-11694-7

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

Autores: Kateřina Melková, Vojtěch Zapletal, Séverine Jansen, Erik Nomilner, Milan Zachrdla, Jozef Hritz, Jiří Nováček, Markus Zweckstetter, Malene R. Jensen, Martin Blackledge, Lukáš Žídek
Publicado en: Journal of Biological Chemistry, Edición 293/34, 2018, Página(s) 13297-13309, ISSN 0021-9258
Editor: 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

Autores: Monika Hermanová, Pavlína Havranová-Vidláková, Anna Ondráčková, Swathi Senthil Kumar, Richard Bowater, Miroslav Fojta
Publicado en: Electroanalysis, Edición 31/2, 2019, Página(s) 246-255, ISSN 1040-0397
Editor: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/elan.201800452

Asymmetric bifurcated halogen bonds

Autores: Martin Novák, Cina Foroutan-Nejad, Radek Marek
Publicado en: Phys. Chem. Chem. Phys., Edición 14639076, 2015, Página(s) 6440-6450, ISSN 1463-9076
Editor: Royal Society of Chemistry
DOI: 10.1039/c4cp05532b

DNA and RNA Quadruplex-Binding Proteins

Autores: Václav Brázda, Lucia Hároníková, Jack Liao, Miroslav Fojta
Publicado en: International Journal of Molecular Sciences, Edición 14220067, 2014, Página(s) 17493-17517, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms151017493

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation

Autores: S. K. Mishra, M. Kara, M. Zacharias, J. Koca
Publicado en: Glycobiology, Edición 09596658, 2013, Página(s) 70-84, ISSN 0959-6658
Editor: 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

Autores: Kateřina Němcová, Peter Šebest, Luděk Havran, Petr Orság, Miroslav Fojta, Hana Pivoňková
Publicado en: Analytical and Bioanalytical Chemistry, Edición 16182642, 2014, Página(s) 5843-5852, ISSN 1618-2642
Editor: Springer Verlag
DOI: 10.1007/s00216-014-7996-0

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

Autores: Konstantinos Tripsianes, Nam K. Chu, Anders Friberg, Michael Sattler, Christian F. W. Becker
Publicado en: ACS Chemical Biology, Edición 15548929, 2014, Página(s) 347-352, ISSN 1554-8929
Editor: American Chemical Society
DOI: 10.1021/cb400723j

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

Autores: Pavel Kadeřávek, Vojtěch Zapletal, Alžbeta Rabatinová, Libor Krásný, Vladimír Sklenář, Lukáš Žídek
Publicado en: Journal of Biomolecular NMR, Edición 09252738, 2014, Página(s) 193-207, ISSN 0925-2738
Editor: Kluwer Academic Publishers
DOI: 10.1007/s10858-014-9816-4

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

Autores: Jitka Dadová, Petr Orság, Radek Pohl, Marie Brázdová, Miroslav Fojta, Michal Hocek
Publicado en: Angewandte Chemie International Edition, Edición 14337851, 2013, Página(s) 10515-10518, ISSN 1433-7851
Editor: 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

Autores: Daniel Nemecek, Pavel Plevka, Evzen Boura
Publicado en: The Protein Journal, Edición 15723887, 2013, Página(s) 635-640, ISSN 1572-3887
Editor: 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

Autores: Jan Vícha, Michael Patzschke, Radek Marek
Publicado en: Physical Chemistry Chemical Physics, Edición 14639076, 2013, Página(s) 7740, ISSN 1463-9076
Editor: 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

Autores: Ales Danhel, Veronika Raindlova, Ludek Havran, Jiri Barek, Michal Hocek, Miroslav Fojta
Publicado en: Electrochimica Acta, Edición 00134686, 2014, Página(s) 348-357, ISSN 0013-4686
Editor: Pergamon Press Ltd.
DOI: 10.1016/j.electacta.2014.02.137

Instability restricts signaling of multiple fibroblast growth factors

Autores: 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
Publicado en: Cellular and Molecular Life Sciences, Edición 1420682X, 2015, Página(s) 2445-2459, ISSN 1420-682X
Editor: Birkhauser Verlag
DOI: 10.1007/s00018-015-1856-8

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

Autores: K. Tripsianes, A. Friberg, C. Barrandon, M. Brooks, H. van Tilbeurgh, B. Seraphin, M. Sattler
Publicado en: Journal of Biological Chemistry, Edición 00219258, 2014, Página(s) 28640-28650, ISSN 0021-9258
Editor: 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

Autores: Zdeněk Kříž, Jiří Klusák, Zdena Krištofíková, Jaroslav Koča
Publicado en: PLoS ONE, Edición 19326203, 2013, Página(s) e62914, ISSN 1932-6203
Editor: 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

Autores: Jiří Nováček, Lubomír Janda, Radka Dopitová, Lukáš Žídek, Vladimír Sklenář
Publicado en: Journal of Biomolecular NMR, Edición 09252738, 2013, Página(s) 291-301, ISSN 0925-2738
Editor: 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

Autores: Ales Danhel, Veronika Raindlova, Ludek Havran, Hana Pivonkova, Michal Hocek, Miroslav Fojta
Publicado en: Electrochimica Acta, Edición 00134686, 2014, Página(s) 122-131, ISSN 0013-4686
Editor: Pergamon Press Ltd.
DOI: 10.1016/j.electacta.2013.09.147

High-quality and universal empirical atomic charges for chemoinformatics applications

Autores: Stanislav Geidl, Tomáš Bouchal, Tomáš Raček, Radka Svobodová Vařeková, Václav Hejret, Aleš Křenek, Ruben Abagyan, Jaroslav Koča
Publicado en: Journal of Cheminformatics, Edición 17582946, 2015, ISSN 1758-2946
Editor: 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

Autores: Cina Foroutan-Nejad, Radek Marek
Publicado en: Phys. Chem. Chem. Phys., Edición 14639076, 2014, Página(s) 2508-2514, ISSN 1463-9076
Editor: 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

Autores: Lukáš Fojt, Miroslav Fojta, Bohumír Grüner, Radim Vespalec
Publicado en: Journal of Electroanalytical Chemistry, Edición 15726657, 2013, Página(s) 38-42, ISSN 1572-6657
Editor: Elsevier BV
DOI: 10.1016/j.jelechem.2013.08.016

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

Autores: A. Nyarko, Y. Song, J. Novacek, L. Zidek, E. Barbar
Publicado en: Journal of Biological Chemistry, Edición 00219258, 2013, Página(s) 2614-2622, ISSN 0021-9258
Editor: 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

Autores: Helena Konvalinová, Zuzana Dvořáková, Daniel Renčiuk, Klára Bednářová, Iva Kejnovská, Lukáš Trantírek, Michaela Vorlíčková, Janos Sagi
Publicado en: Biochimie, Edición 03009084, 2015, Página(s) 15-25, ISSN 0300-9084
Editor: Elsevier BV
DOI: 10.1016/j.biochi.2015.07.013

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

Autores: Sophia Bazzi, Jan Novotný, Yevgen P. Yurenko, Radek Marek
Publicado en: Chemistry - A European Journal, Edición 09476539, 2015, Página(s) 9414-9425, ISSN 0947-6539
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201500743

Expression of FGF19 in human embryonic stem cells

Autores: Pavel Krejci, Michaela Kunova, Iva Kubikova, Lukas Trantirek, Alois Kozubik, Petr Dvorak
Publicado en: STEM CELLS, Edición 10665099, 2013, Página(s) 2582-2584, ISSN 1066-5099
Editor: 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

Autores: Pavlína Vidláková, Hana Pivoňková, Miroslav Fojta, Luděk Havran
Publicado en: Monatshefte für Chemie - Chemical Monthly, Edición 00269247, 2015, Página(s) 839-847, ISSN 0026-9247
Editor: Springer Verlag
DOI: 10.1007/s00706-015-1435-6

Biophysical and electrochemical studies of protein–nucleic acid interactions

Autores: Richard P. Bowater, Andrew M. Cobb, Hana Pivonkova, Ludek Havran, Miroslav Fojta
Publicado en: Monatshefte für Chemie - Chemical Monthly, Edición 00269247, 2015, Página(s) 723-739, ISSN 0026-9247
Editor: 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

Autores: Tomáš Trnka, Stanislav Kozmon, Igor Tvaroška, Jaroslav Koča
Publicado en: PLOS Computational Biology, Edición 1553734X, 2015, Página(s) e1004061, ISSN 1553-734X
Editor: 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

Autores: Jan Vícha, Cina Foroutan-Nejad, Tomasz Pawlak, Markéta L. Munzarová, Michal Straka, Radek Marek
Publicado en: Journal of Chemical Theory and Computation, Edición 15499618, 2015, Página(s) 1509-1517, ISSN 1549-9618
Editor: 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

Autores: Jiří Emmer, Andrea Vavrinská, Vladimír Sychrovský, Ladislav Benda, Zdeněk Kříž, Jaroslav Koča, Rolf Boelens, Vladimír Sklenář, Lukáš Trantírek
Publicado en: Journal of Biomolecular NMR, Edición 09252738, 2013, Página(s) 59-70, ISSN 0925-2738
Editor: 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

Autores: Peter Šebest, Marie Brázdová, Miroslav Fojta, Hana Pivoňková
Publicado en: International Journal of Molecular Sciences, Edición 14220067, 2015, Página(s) 3163-3177, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms16023163

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

Autores: Petra Ménová, Hana Cahová, Medard Plucnara, Luděk Havran, Miroslav Fojta, Michal Hocek
Publicado en: Chemical Communications, Edición 13597345, 2013, Página(s) 4652, ISSN 1359-7345
Editor: Royal Society of Chemistry
DOI: 10.1039/c3cc41438h

A novel variant of FGFR3 causes proportionate short stature

Autores: 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
Publicado en: European Journal of Endocrinology, Edición 08044643, 2015, Página(s) 763-770, ISSN 0804-4643
Editor: BioScientifica Ltd.
DOI: 10.1530/EJE-14-0945

In-Cell NMR and EPR Spectroscopy of Biomacromolecules

Autores: Robert Hänsel, Laura M. Luh, Ivan Corbeski, Lukáš Trantirek, Volker Dötsch
Publicado en: Angewandte Chemie International Edition, Edición 14337851, 2014, Página(s) 10300-10314, ISSN 1433-7851
Editor: 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

Autores: Jitka Dadová, Pavlína Vidláková, Radek Pohl, Luděk Havran, Miroslav Fojta, Michal Hocek
Publicado en: The Journal of Organic Chemistry, Edición 00223263, 2013, Página(s) 9627-9637, ISSN 0022-3263
Editor: American Chemical Society
DOI: 10.1021/jo4011574

Molecular Basis for Coordinating Transcription Termination with Noncoding RNA Degradation

Autores: Agnieszka Tudek, Odil Porrua, Tomasz Kabzinski, Michael Lidschreiber, Karel Kubicek, Andrea Fortova, François Lacroute, Stepanka Vanacova, Patrick Cramer, Richard Stefl, Domenico Libri
Publicado en: Molecular Cell, Edición 10972765, 2014, Página(s) 467-481, ISSN 1097-2765
Editor: Cell Press
DOI: 10.1016/j.molcel.2014.05.031

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

Autores: Manju Kumari, Stanislav Kozmon, Petr Kulhánek, Jakub Štepán, Igor Tvaroška, Jaroslav Koča
Publicado en: The Journal of Physical Chemistry B, Edición 15206106, 2015, Página(s) 4371-4381, ISSN 1520-6106
Editor: American Chemical Society
DOI: 10.1021/jp511235f

Autores: Pavel Kadeřávek, Sarina Grutsch, Nicola Salvi, Martin Tollinger, Lukáš Žídek, Geoffrey Bodenhausen, Fabien Ferrage
Publicado en: Journal of Biomolecular NMR, Edición 09252738, 2015, Página(s) 353-365, ISSN 0925-2738
Editor: 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

Autores: Veronika Papoušková, Pavel Kadeřávek, Olga Otrusinová, Alžbeta Rabatinová, Hana Šanderová, Jiří Nováček, Libor Krásný, Vladimír Sklenář, Lukáš Žídek
Publicado en: ChemBioChem, Edición 14394227, 2013, Página(s) 1772-1779, ISSN 1439-4227
Editor: 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

Autores: Jaromír Toušek, Michal Straka, Vladimír Sklenář, Radek Marek
Publicado en: The Journal of Physical Chemistry A, Edición 10895639, 2013, Página(s) 661-669, ISSN 1089-5639
Editor: American Chemical Society
DOI: 10.1021/jp310470f

High-Resolution Insight into G-Overhang Architecture

Autores: Robert Hänsel, Frank Löhr, Lukáš Trantirek, Volker Dötsch
Publicado en: Journal of the American Chemical Society, Edición 00027863, 2013, Página(s) 2816-2824, ISSN 0002-7863
Editor: American Chemical Society
DOI: 10.1021/ja312403b

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

Autores: R. S. Va ekova, D. Jaiswal, D. Sehnal, C.-M. Ionescu, S. Geidl, L. Pravda, V. Horsky, M. Wimmerova, J. Ko a
Publicado en: Nucleic Acids Research, Edición 03051048, 2014, Página(s) W227-W233, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gku426

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

Autores: Josef Houser, Jan Komarek, Gianluca Cioci, Annabelle Varrot, Anne Imberty, Michaela Wimmerova
Publicado en: Acta Crystallographica Section D Biological Crystallography, Edición 13990047, 2015, Página(s) 442-453, ISSN 1399-0047
Editor: 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

Autores: A. Rabatinova, H. Sanderova, J. Jirat Matejckova, J. Korelusova, L. Sojka, I. Barvik, V. Papouskova, V. Sklenar, L. Zidek, L. Krasny
Publicado en: Journal of Bacteriology, Edición 00219193, 2013, Página(s) 2603-2611, ISSN 0021-9193
Editor: 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

Autores: Petr Stadlbauer, Petra Kührová, Pavel Banáš, Jaroslav Koča, Giovanni Bussi, Lukáš Trantírek, Michal Otyepka, Jiří Šponer
Publicado en: Nucleic Acids Research, Edición 03051048, 2015, Página(s) gkv994, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkv994

Extended molecular dynamics of a c-kit promoter quadruplex

Autores: Barira Islam, Petr Stadlbauer, Miroslav Krepl, Jaroslav Koca, Stephen Neidle, Shozeb Haider, Jiri Sponer
Publicado en: Nucleic Acids Research, Edición 03051048, 2015, Página(s) 8673-8693, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkv785

New sensitive detection method for lectin hemagglutination using microscopy

Autores: Lenka Adamová, Lenka Malinovská, Michaela Wimmerová
Publicado en: Microscopy Research and Technique, Edición 1059910X, 2014, Página(s) 841-849, ISSN 1059-910X
Editor: John Wiley & Sons Inc.
DOI: 10.1002/jemt.22407

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

Autores: D. Ustianenko, D. Hrossova, D. Potesil, K. Chalupnikova, K. Hrazdilova, J. Pachernik, K. Cetkovska, S. Uldrijan, Z. Zdrahal, S. Vanacova
Publicado en: RNA, Edición 13558382, 2013, Página(s) 1632-1638, ISSN 1355-8382
Editor: Cold Spring Harbor Laboratory Press
DOI: 10.1261/rna.040055.113

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

Autores: Zdeněk Kříž, Jan Adam, Jana Mrázková, Petros Zotos, Thomais Chatzipavlou, Michaela Wimmerová, Jaroslav Koča
Publicado en: Journal of Computer-Aided Molecular Design, Edición 0920654X, 2014, Página(s) 951-960, ISSN 0920-654X
Editor: Kluwer Academic Publishers
DOI: 10.1007/s10822-014-9774-7

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

Autores: Shivaji S. Kadam, Lukáš Maier, Tomáš Šolomek, Marek Nečas, Karel Šmejkal, Jiří Dostál, Vladimír Sklenář, Radek Marek
Publicado en: Journal of Physical Organic Chemistry, Edición 08943230, 2013, Página(s) 814-821, ISSN 0894-3230
Editor: John Wiley & Sons Inc.
DOI: 10.1002/poc.3175

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

Autores: 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
Publicado en: PLOS ONE, Edición 19326203, 2015, Página(s) e0119899, ISSN 1932-6203
Editor: 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

Autores: Marie Brázdová, Lucie Navrátilová, Vlastimil Tichý, Kateřina Němcová, Matej Lexa, Roman Hrstka, Petr Pečinka, Matej Adámik, Borivoj Vojtesek, Emil Paleček, Wolfgang Deppert, Miroslav Fojta
Publicado en: PLoS ONE, Edición 19326203, 2013, Página(s) e59567, ISSN 1932-6203
Editor: 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?

Autores: Stanislav Geidl, Radka Svobodová Vařeková, Veronika Bendová, Lukáš Petrusek, Crina-Maria Ionescu, Zdeněk Jurka, Ruben Abagyan, Jaroslav Koča
Publicado en: Journal of Chemical Information and Modeling, Edición 15499596, 2015, Página(s) 1088-1097, ISSN 1549-9596
Editor: American Chemical Society
DOI: 10.1021/ci500758w

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

Autores: Jitka Dadová, Milan Vrábel, Matej Adámik, Marie Brázdová, Radek Pohl, Miroslav Fojta, Michal Hocek
Publicado en: Chemistry - A European Journal, Edición 09476539, 2015, Página(s) 16091-16102, ISSN 0947-6539
Editor: 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

Autores: Igor Tvaroška, Stanislav Kozmon, Michaela Wimmerová, Jaroslav Koča
Publicado en: Chemistry - A European Journal, Edición 09476539, 2013, Página(s) 8153-8162, ISSN 0947-6539
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201300383

Tailoring the properties of quadruplex nucleobases for biological and nanomaterial applications

Autores: Jan Novotný, Yevgen P. Yurenko, Petr Kulhánek, Radek Marek
Publicado en: Physical Chemistry Chemical Physics, Edición 14639076, 2014, Página(s) 15241, ISSN 1463-9076
Editor: Royal Society of Chemistry
DOI: 10.1039/c4cp00541d

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules

Autores: Crina-Maria Ionescu, David Sehnal, Francesco L. Falginella, Purbaj Pant, Lukáš Pravda, Tomáš Bouchal, Radka Svobodová Vařeková, Stanislav Geidl, Jaroslav Koča
Publicado en: Journal of Cheminformatics, Edición 17582946, 2015, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/s13321-015-0099-x

Toward a Consistent Interpretation of the QTAIM: Tortuous Link between Chemical Bonds, Interactions, and Bond/Line Paths

Autores: Cina Foroutan-Nejad, Shant Shahbazian, Radek Marek
Publicado en: Chemistry - A European Journal, Edición 09476539, 2014, Página(s) 10140-10152, ISSN 0947-6539
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201402177

Retro operation on the Trp-cage miniprotein sequence produces an unstructured molecule capable of folding similar to the original only upon 2,2,2-trifluoroethanol addition

Autores: J. Vym tal, S. R. Bathula, J. erny, R. Chaloupkova, L. idek, V. Sklena , J. Vondra ek
Publicado en: Protein Engineering Design and Selection, Edición 17410126, 2014, Página(s) 463-472, ISSN 1741-0126
Editor: Oxford University Press
DOI: 10.1093/protein/gzu046

Multi-center covalency: revisiting the nature of anion–π interactions

Autores: Cina Foroutan-Nejad, Zahra Badri, Radek Marek
Publicado en: Phys. Chem. Chem. Phys., Edición 14639076, 2015, Página(s) 30670-30679, ISSN 1463-9076
Editor: Royal Society of Chemistry
DOI: 10.1039/c5cp05777a

Dimeric Pd(II) and Pt(II) chloride organometallics with 2-phenylpyridine and their solvolysis in dimethylsulfoxide

Autores: Tomasz Pawlak, Daria Niedzielska, Jan Vícha, Radek Marek, Leszek Pazderski
Publicado en: Journal of Organometallic Chemistry, Edición 0022328X, 2014, Página(s) 58-66, ISSN 0022-328X
Editor: Elsevier BV
DOI: 10.1016/j.jorganchem.2014.02.016

Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes

Autores: Sushil K. Mishra, Gaetano Calabró, Hannes H. Loeffler, Julien Michel, Jaroslav Koča
Publicado en: Journal of Chemical Theory and Computation, Edición 15499618, 2015, Página(s) 3333-3345, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/acs.jctc.5b00159

Synthesis and Tautomerism of Substituted Pyrazolo[4,3- c ]pyrazoles

Autores: Shivaji S. Kadam, Lukáš Maier, Ioannis Kostakis, Nicole Pouli, Jaromír Toušek, Marek Nečas, Panagiotis Marakos, Radek Marek
Publicado en: European Journal of Organic Chemistry, Edición 1434193X, 2013, Página(s) 6811-6822, ISSN 1434-193X
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/ejoc.201300606

Intermolecular Interactions in Crystalline Theobromine as Reflected in Electron Deformation Density and 13 C NMR Chemical Shift Tensors

Autores: Kateřina Bouzková, Martin Babinský, Lucie Novosadová, Radek Marek
Publicado en: Journal of Chemical Theory and Computation, Edición 15499618, 2013, Página(s) 2629-2638, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/ct400209b

Adamantane-bearing benzylamines and benzylamides: novel building blocks for supramolecular systems with finely tuned binding properties towards β-cyclodextrin

Autores: Michal Rouchal, Alena Matelová, Fabiana Pires de Carvalho, Robert Bernat, Dragan Grbić, Ivo Kuřitka, Martin Babinský, Radek Marek, Richard Čmelík, Robert Vícha
Publicado en: Supramolecular Chemistry, Edición 10610278, 2013, Página(s) 349-361, ISSN 1061-0278
Editor: Taylor & Francis
DOI: 10.1080/10610278.2013.783916

Benzofurazane as a New Redox Label for Electrochemical Detection of DNA: Towards Multipotential Redox Coding of DNA Bases

Autores: Jana Balintová, Medard Plucnara, Pavlína Vidláková, Radek Pohl, Luděk Havran, Miroslav Fojta, Michal Hocek
Publicado en: Chemistry - A European Journal, Edición 09476539, 2013, Página(s) 12720-12731, ISSN 0947-6539
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201301868

Functional Analysis of Dishevelled-3 Phosphorylation Identifies Distinct Mechanisms Driven by Casein Kinase 1 and Frizzled5

Autores: O. Bernatik, K. edova, C. Schille, R. S. Ganji, I. ervenka, L. Trantirek, A. Schambony, Z. Zdrahal, V. Bryja
Publicado en: Journal of Biological Chemistry, Edición 00219258, 2014, Página(s) 23520-23533, ISSN 0021-9258
Editor: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.M114.590638

Cloning, expression and purification of the human Islet Amyloid Polypeptide (hIAPP) from Escherichia coli

Autores: Diana C. Rodriguez Camargo, Konstantinos Tripsianes, Tobias G. Kapp, Joaquim Mendes, Jasmin Schubert, Burghard Cordes, Bernd Reif
Publicado en: Protein Expression and Purification, Edición 10465928, 2015, Página(s) 49-56, ISSN 1046-5928
Editor: Academic Press
DOI: 10.1016/j.pep.2014.10.012

Electrochemistry of parent and exo-skeletally substituted icosahedral monocarba and dicarbaboranes and their derivatives at the graphite carbon electrode in aqueous phosphate buffers

Autores: Lukáš Fojt, Miroslav Fojta, Bohumír Grüner, Radim Vespalec
Publicado en: Journal of Electroanalytical Chemistry, Edición 15726657, 2014, Página(s) 16-19, ISSN 1572-6657
Editor: Elsevier BV
DOI: 10.1016/j.jelechem.2014.07.023

Crystallization and preliminary X-ray crystallographic analysis of recombinant β-mannosidase from Aspergillus niger

Autores: Gabriel Demo, Barbora Fliedrová, Lenka Weignerová, Michaela Wimmerová
Publicado en: Acta Crystallographica Section F Structural Biology and Crystallization Communications, Edición 17443091, 2013, Página(s) 288-291, ISSN 1744-3091
Editor: International Union of Crystallography
DOI: 10.1107/S1744309113002522

Loss of loop adenines alters human telomere d[AG3(TTAG3)3] quadruplex folding

Autores: M. Babinsky, R. Fiala, I. Kejnovska, K. Bedna ova, R. Marek, J. Sagi, V. Sklena , M. Vorli kova
Publicado en: Nucleic Acids Research, Edición 03051048, 2014, Página(s) 14031-14041, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gku1245

Mechanism of Spin–Orbit Effects on the Ligand NMR Chemical Shift in Transition-Metal Complexes: Linking NMR to EPR

Autores: Jan Vícha, Michal Straka, Markéta L. Munzarová, Radek Marek
Publicado en: Journal of Chemical Theory and Computation, Edición 15499618, 2014, Página(s) 1489-1499, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/ct400726y

Stabilization of the β-hairpin in Mason-Pfizer monkey virus capsid protein- a critical step for infectivity

Autores: Martin Obr, Romana Hadravová, Michal Doležal, Ivana Křžová, Veronika Papoušková, Lukáš Žídek, Richard Hrabal, Tomáš Ruml, Michaela Rumlová
Publicado en: Retrovirology, Edición 17424690, 2014, ISSN 1742-4690
Editor: BioMed Central
DOI: 10.1186/s12977-014-0094-8

Unwilling U–U bonding in U 2 @C 80 : cage-driven metal–metal bonds in di-uranium fullerenes

Autores: Cina Foroutan-Nejad, Jan Vícha, Radek Marek, Michael Patzschke, Michal Straka
Publicado en: Phys. Chem. Chem. Phys., Edición 14639076, 2015, Página(s) 24182-24192, ISSN 1463-9076
Editor: Royal Society of Chemistry
DOI: 10.1039/c5cp04280a

129 Xe NMR chemical shift in Xe@C 60 calculated at experimental conditions: Essential role of the relativity, dynamics, and explicit solvent

Autores: Stanislav Standara, Petr Kulhánek, Radek Marek, Michal Straka
Publicado en: Journal of Computational Chemistry, Edición 01928651, 2013, Página(s) 1890-1898, ISSN 0192-8651
Editor: John Wiley & Sons Inc.
DOI: 10.1002/jcc.23334

Molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43

Autores: Peter J Lukavsky, Dalia Daujotyte, James R Tollervey, Jernej Ule, Cristiana Stuani, Emanuele Buratti, Francisco E Baralle, Fred F Damberger, Frédéric H-T Allain
Publicado en: Nature Structural & Molecular Biology, Edición 15459993, 2013, Página(s) 1443-1449, ISSN 1545-9993
Editor: Nature Publishing Group
DOI: 10.1038/nsmb.2698

Intermediate filament-associated cytolinker plectin 1c destabilizes microtubules in keratinocytes

Autores: R. G. Valencia, G. Walko, L. Janda, J. Novacek, E. Mihailovska, S. Reipert, K. Andra-Marobela, G. Wiche
Publicado en: Molecular Biology of the Cell, Edición 10591524, 2013, Página(s) 768-784, ISSN 1059-1524
Editor: American Society for Cell Biology
DOI: 10.1091/mbc.E12-06-0488

All-Metal Aromaticity: Revisiting the Ring Current Model among Transition Metal Clusters

Autores: Zahra Badri, Shubhrodeep Pathak, Heike Fliegl, Parviz Rashidi-Ranjbar, Radovan Bast, Radek Marek, Cina Foroutan-Nejad, Kenneth Ruud
Publicado en: Journal of Chemical Theory and Computation, Edición 15499618, 2013, Página(s) 4789-4796, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/ct4007184

Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta

Autores: Zaiyong Zhang, Justin Porter, Konstantinos Tripsianes, Oliver F. Lange
Publicado en: Journal of Biomolecular NMR, Edición 09252738, 2014, Página(s) 135-145, ISSN 0925-2738
Editor: Kluwer Academic Publishers
DOI: 10.1007/s10858-014-9832-4

Protein engineering study of -mannosidase to set up a potential chemically efficient biocatalyst

Autores: G. Demo, V. Horska, B. Fliedrova, J. t pan, J. Ko a, L. Weignerova, V. K en, M. Wimmerova
Publicado en: Glycobiology, Edición 09596658, 2014, Página(s) 1301-1311, ISSN 0959-6658
Editor: Oxford University Press
DOI: 10.1093/glycob/cwu074

X-ray vs. NMR structure of N-terminal domain of δ-subunit of RNA polymerase

Autores: Gabriel Demo, Veronika Papoušková, Jan Komárek, Pavel Kadeřávek, Olga Otrusinová, Pavel Srb, Alžbeta Rabatinová, Libor Krásný, Lukáš Žídek, Vladimír Sklenář, Michaela Wimmerová
Publicado en: Journal of Structural Biology, Edición 10478477, 2014, Página(s) 174-186, ISSN 1047-8477
Editor: Academic Press
DOI: 10.1016/j.jsb.2014.06.001

A Soluble Fucose-Specific Lectin from Aspergillus fumigatus Conidia - Structure, Specificity and Possible Role in Fungal Pathogenicity

Autores: Josef Houser, Jan Komarek, Nikola Kostlanova, Gianluca Cioci, Annabelle Varrot, Sheena C. Kerr, Martina Lahmann, Viviane Balloy, John V. Fahy, Michel Chignard, Anne Imberty, Michaela Wimmerova
Publicado en: PLoS ONE, Edición 19326203, 2013, Página(s) e83077, ISSN 1932-6203
Editor: Public Library of Science
DOI: 10.1371/journal.pone.0083077

Electrochemical Activity of Wedelolactone and Probing its Interaction with DNA Using Voltammetry at a Carbon Electrode

Autores: Jiří Červeň, Luděk Havran, Petr Pečinka, Miroslav Fojta
Publicado en: Electroanalysis, Edición 10400397, 2015, Página(s) 2268-2271, ISSN 1040-0397
Editor: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/elan.201500177

Enzyme-linked electrochemical detection of DNA fragments amplified by PCR in the presence of a biotinylated deoxynucleoside triphosphate using disposable pencil graphite electrodes

Autores: Lucia Hároníková, Jan Špaček, Medard Plucnara, Petra Horáková, Hana Pivoňková, Luděk Havran, Arzum Erdem, Miroslav Fojta
Publicado en: Monatshefte für Chemie - Chemical Monthly, Edición 00269247, 2015, Página(s) 849-855, ISSN 0026-9247
Editor: Springer Verlag
DOI: 10.1007/s00706-015-1436-5

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AHP2, a signal transmitter protein from Arabidopsis thaliana

Autores: Oksana Degtjarik, Radka Dopitova, Sandra Puehringer, Eliska Nejedla, Michal Kuty, Manfred S. Weiss, Jan Hejatko, Lubomir Janda, Ivana Kuta Smatanova
Publicado en: Acta Crystallographica Section F Structural Biology and Crystallization Communications, Edición 17443091, 2013, Página(s) 158-161, ISSN 1744-3091
Editor: International Union of Crystallography
DOI: 10.1107/S174430911205186X

Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations

Autores: Konstantinos Gkionis, Holger Kruse, James A. Platts, Arnošt Mládek, Jaroslav Koča, Jiří Šponer
Publicado en: Journal of Chemical Theory and Computation, Edición 15499618, 2014, Página(s) 1326-1340, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/ct4009969

Nucleic Acid Quadruplexes Based on 8-Halo-9-deazaxanthines: Energetics and Noncovalent Interactions in Quadruplex Stems

Autores: Yevgen P. Yurenko, Jan Novotný, Mariusz P. Mitoraj, Vladimir Sklenář, Artur Michalak, Radek Marek
Publicado en: Journal of Chemical Theory and Computation, Edición 15499618, 2014, Página(s) 5353-5365, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/ct5007554

Unique C. elegans telomeric overhang structures reveal the evolutionarily conserved properties of telomeric DNA

Autores: P. kolakova, S. Foldynova-Trantirkova, K. Bedna ova, R. Fiala, M. Vorli kova, L. Trantirek
Publicado en: Nucleic Acids Research, Edición 03051048, 2015, Página(s) 4733-4745, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkv296

Origin of the Thermodynamic Stability of the Polymorph IV of Crystalline Barbituric Acid: Evidence from Solid-State NMR and Electron Density Analyses

Autores: Zahra Badri, Kateřina Bouzková, Cina Foroutan-Nejad, Radek Marek
Publicado en: Crystal Growth & Design, Edición 15287483, 2014, Página(s) 2763-2772, ISSN 1528-7483
Editor: American Chemical Society
DOI: 10.1021/cg401899q

Exploring non-covalent interactions in guanine- and xanthine-based model DNA quadruplex structures: a comprehensive quantum chemical approach

Autores: Yevgen P. Yurenko, Jan Novotný, Vladimir Sklenář, Radek Marek
Publicado en: Phys. Chem. Chem. Phys., Edición 14639076, 2014, Página(s) 2072-2084, ISSN 1463-9076
Editor: Royal Society of Chemistry
DOI: 10.1039/c3cp53875c

G-quadruplex-based structural transitions in 15-mer DNA oligonucleotides varying in lengths of internal oligo(dG) stretches detected by voltammetric techniques

Autores: Pavlína Vidláková, Hana Pivoňková, Iva Kejnovská, Libuše Trnková, Michaela Vorlíčková, Miroslav Fojta, Luděk Havran
Publicado en: Analytical and Bioanalytical Chemistry, Edición 16182642, 2015, Página(s) 5817-5826, ISSN 1618-2642
Editor: Springer Verlag
DOI: 10.1007/s00216-015-8768-1

NMR Determines Transient Structure and Dynamics in the Disordered C-Terminal Domain of WASp Interacting Protein

Autores: Noam Y. Haba, Renana Gross, Jiri Novacek, Hadassa Shaked, Lukas Zidek, Mira Barda-Saad, Jordan H. Chill
Publicado en: Biophysical Journal, Edición 00063495, 2013, Página(s) 481-493, ISSN 0006-3495
Editor: Biophysical Society
DOI: 10.1016/j.bpj.2013.05.046

Detection of p53 Gene by Using Genomagnetic Assay Combined with Carbon Nanotube Modified Disposable Sensor Technology

Autores: Gulsah Congur, Medard Plucnara, Arzum Erdem, Miroslav Fojta
Publicado en: Electroanalysis, Edición 10400397, 2015, Página(s) 1579-1586, ISSN 1040-0397
Editor: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/elan.201400731

Azidophenyl as a click-transformable redox label of DNA suitable for electrochemical detection of DNA–protein interactions

Autores: Jana Balintová, Jan Špaček, Radek Pohl, Marie Brázdová, Luděk Havran, Miroslav Fojta, Michal Hocek
Publicado en: Chem. Sci., Edición 20416520, 2015, Página(s) 575-587, ISSN 2041-6520
Editor: Royal Society of Chemistry
DOI: 10.1039/c4sc01906g

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

Autores: David Sehnal, Radka Svobodová Vařeková, Karel Berka, Lukáš Pravda, Veronika Navrátilová, Pavel Banáš, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koča
Publicado en: Journal of Cheminformatics, Edición 17582946, 2013, Página(s) 39, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/1758-2946-5-39

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

Autores: Petr Stadlbauer, Lukáš Trantírek, Thomas E. Cheatham, Jaroslav Koča, Jiří Šponer
Publicado en: Biochimie, Edición 03009084, 2014, Página(s) 22-35, ISSN 0300-9084
Editor: Elsevier BV
DOI: 10.1016/j.biochi.2014.07.009

Anatomy of enzyme channels

Autores: Lukáš Pravda, Karel Berka, Radka Svobodová Vařeková, David Sehnal, Pavel Banáš, Roman A Laskowski, Jaroslav Koča, Michal Otyepka
Publicado en: BMC Bioinformatics, Edición 14712105, 2014, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.1186/s12859-014-0379-x

Antibodies against CKI1RD, a receiver domain of the sensor histidine kinase in Arabidopsis thaliana: From antigen preparation to in planta immunolocalization

Autores: Petra Borkovcová, Blanka Pekárová, Martina Válková, Radka Dopitová, Břetislav Brzobohatý, Lubomír Janda, Jan Hejátko
Publicado en: Phytochemistry, Edición 00319422, 2014, Página(s) 6-15, ISSN 0031-9422
Editor: Elsevier BV
DOI: 10.1016/j.phytochem.2014.01.007

The activation of N-glycosidic bond cleavage performed by base-excision repair enzyme hOGG1; theoretical study of the role of Lys 249 residue in activation of G, OxoG and FapyG

Autores: Jakub Šebera, Lukáš Trantírek, Yoshiyuki Tanaka, Radim Nencka, Jiří Fukal, Vladimír Sychrovský
Publicado en: RSC Adv., Edición 20462069, 2014, Página(s) 44043-44051, ISSN 2046-2069
Editor: Royal Society of Chemistry
DOI: 10.1039/c4ra08278h

NMR assignment of intrinsically disordered self-processing module of the FrpC protein of Neisseria meningitidis

Autores: Vojtěch Kubáň, Jiří Nováček, Ladislav Bumba, Lukáš Žídek
Publicado en: Biomolecular NMR Assignments, Edición 18742718, 2015, Página(s) 435-440, ISSN 1874-2718
Editor: Springer Verlag
DOI: 10.1007/s12104-015-9625-z

Structure, solvent, and relativistic effects on the NMR chemical shifts in square-planar transition-metal complexes: assessment of DFT approaches

Autores: Jan Vícha, Jan Novotný, Michal Straka, Michal Repisky, Kenneth Ruud, Stanislav Komorovsky, Radek Marek
Publicado en: Phys. Chem. Chem. Phys., Edición 14639076, 2015, Página(s) 24944-24955, ISSN 1463-9076
Editor: Royal Society of Chemistry
DOI: 10.1039/c5cp04214c

Bicaudal-D uses a parallel, homodimeric coiled coil with heterotypic registry to coordinate recruitment of cargos to dynein

Autores: Y. Liu, H. K. Salter, A. N. Holding, C. M. Johnson, E. Stephens, P. J. Lukavsky, J. Walshaw, S. L. Bullock
Publicado en: Genes & Development, Edición 08909369, 2013, Página(s) 1233-1246, ISSN 0890-9369
Editor: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gad.212381.112

Interpretation of Crystal Effects on NMR Chemical Shift Tensors: Electron and Shielding Deformation Densities

Autores: Martin Babinský, Kateřina Bouzková, Matej Pipíška, Lucie Novosadová, Radek Marek
Publicado en: The Journal of Physical Chemistry A, Edición 10895639, 2013, Página(s) 497-503, ISSN 1089-5639
Editor: American Chemical Society
DOI: 10.1021/jp310967b

Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method

Autores: Crina-Maria Ionescu, Stanislav Geidl, Radka Svobodová Vařeková, Jaroslav Koča
Publicado en: Journal of Chemical Information and Modeling, Edición 15499596, 2013, Página(s) 2548-2558, ISSN 1549-9596
Editor: American Chemical Society
DOI: 10.1021/ci400448n

Fluorescent Cellular Assay for Screening Agents Inhibiting Pseudomonas aeruginosa Adherence

Autores: Libuše Nosková, Božena Kubíčková, Lucie Vašková, Barbora Bláhová, Michaela Wimmerová, Marie Stiborová, Petr Hodek
Publicado en: Sensors, Edición 14248220, 2015, Página(s) 1945-1953, ISSN 1424-8220
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/s150101945

Methoxyphenol and Dihydrobenzofuran as Oxidizable Labels for Electrochemical Detection of DNA

Autores: Anna Simonova, Jana Balintová, Radek Pohl, Luděk Havran, Miroslav Fojta, Michal Hocek
Publicado en: ChemPlusChem, Edición 21926506, 2014, Página(s) n/a-n/a, ISSN 2192-6506
Editor: Wiley-VCH Verlag
DOI: 10.1002/cplu.201402194

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank

Autores: David Sehnal, Lukáš Pravda, Radka Svobodová Vařeková, Crina-Maria Ionescu, Jaroslav Koča
Publicado en: Nucleic Acids Research, Edición 03051048, 2015, Página(s) W383-W388, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkv561

ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank

Autores: D. Sehnal, R. Svobodova Va ekova, L. Pravda, C.-M. Ionescu, S. Geidl, V. Horsky, D. Jaiswal, M. Wimmerova, J. Ko a
Publicado en: Nucleic Acids Research, Edición 03051048, 2015, Página(s) D369-D375, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gku1118

Toward optimal-resolution NMR of intrinsically disordered proteins

Autores: Jiří Nováček, Lukáš Žídek, Vladimír Sklenář
Publicado en: Journal of Magnetic Resonance, Edición 10907807, 2014, Página(s) 41-52, ISSN 1090-7807
Editor: Academic Press
DOI: 10.1016/j.jmr.2013.12.008

Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease

Autores: Carolina Estarellas, Michal Otyepka, Jaroslav Koča, Pavel Banáš, Miroslav Krepl, Jiří Šponer
Publicado en: Biochimica et Biophysica Acta (BBA) - General Subjects, Edición 03044165, 2015, Página(s) 1072-1090, ISSN 0304-4165
Editor: Elsevier BV
DOI: 10.1016/j.bbagen.2014.10.021

RBM7 subunit of the NEXT complex binds U-rich sequences and targets 3'-end extended forms of snRNAs

Autores: D. Hrossova, T. Sikorsky, D. Potesil, M. Bartosovic, J. Pasulka, Z. Zdrahal, R. Stefl, S. Vanacova
Publicado en: Nucleic Acids Research, Edición 03051048, 2015, Página(s) 4236-4248, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkv240

Design of Stereoelectronically Promoted Super Lewis Acids and Unprecedented Chemistry of Their Complexes

Autores: Cina Foroutan-Nejad, Jan Vicha, Radek Marek
Publicado en: Chemistry - A European Journal, Edición 09476539, 2014, Página(s) 11584-11590, ISSN 0947-6539
Editor: 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

Autores: Yevgen P. Yurenko, Jan Novotný, Vladimir Sklenář, Radek Marek
Publicado en: Chemistry - A European Journal, Edición 09476539, 2015, Página(s) 17933-17943, ISSN 0947-6539
Editor: 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

Autores: Mainak Debnath, Arpan Dutta, Surajit Biswas, Kalyan Kumar Das, Hon Man Lee, Jan Vícha, Radek Marek, Jaromir Marek, Mahammad Ali
Publicado en: Polyhedron, Edición 02775387, 2013, Página(s) 189-198, ISSN 0277-5387
Editor: Pergamon Press
DOI: 10.1016/j.poly.2013.07.013

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

Autores: Matej Zábrady, Vendula Hrdinová, Bruno Müller, Udo Conrad, Jan Hejátko, Lubomír Janda
Publicado en: PLoS ONE, Edición 19326203, 2014, Página(s) e109875, ISSN 1932-6203
Editor: Public Library of Science
DOI: 10.1371/journal.pone.0109875

Predicting p Ka values from EEM atomic charges

Autores: Radka Vařeková, Stanislav Geidl, Crina-Maria Ionescu, Ondřej Skřehota, Tomáš Bouchal, David Sehnal, Ruben Abagyan, Jaroslav Koča
Publicado en: Journal of Cheminformatics, Edición 17582946, 2013, Página(s) 18, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/1758-2946-5-18

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

Autores: Zahra Badri, Cina Foroutan-Nejad, Jiri Kozelka, Radek Marek
Publicado en: Phys. Chem. Chem. Phys., Edición 14639076, 2015, Página(s) 26183-26190, ISSN 1463-9076
Editor: Royal Society of Chemistry
DOI: 10.1039/c5cp04489h

Enzyme-linked electrochemical DNA ligation assay using magnetic beads

Autores: Eva Stejskalová, Petra Horáková, Jan Vacek, Richard P. Bowater, Miroslav Fojta
Publicado en: Analytical and Bioanalytical Chemistry, Edición 16182642, 2014, Página(s) 4129-4136, ISSN 1618-2642
Editor: Springer Verlag
DOI: 10.1007/s00216-014-7811-y

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