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

Deliverables

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

Publications

Implementing efficient concerted rotations using Mathematica and C code⋆

Author(s): Luca Tubiana, Miroslav Jurásek, Ivan Coluzza
Published in: The European Physical Journal E, Issue 41/7, 2018, ISSN 1292-8941
Publisher: Springer Verlag
DOI: 10.1140/epje/i2018-11694-7

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

Author(s): Kateřina Melková, Vojtěch Zapletal, Séverine Jansen, Erik Nomilner, Milan Zachrdla, Jozef Hritz, Jiří Nováček, Markus Zweckstetter, Malene R. Jensen, Martin Blackledge, Lukáš Žídek
Published in: Journal of Biological Chemistry, Issue 293/34, 2018, Page(s) 13297-13309, ISSN 0021-9258
Publisher: 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

Author(s): Monika Hermanová, Pavlína Havranová-Vidláková, Anna Ondráčková, Swathi Senthil Kumar, Richard Bowater, Miroslav Fojta
Published in: Electroanalysis, Issue 31/2, 2019, Page(s) 246-255, ISSN 1040-0397
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/elan.201800452

Asymmetric bifurcated halogen bonds

Author(s): Martin Novák, Cina Foroutan-Nejad, Radek Marek
Published in: Phys. Chem. Chem. Phys., Issue 14639076, 2015, Page(s) 6440-6450, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/c4cp05532b

DNA and RNA Quadruplex-Binding Proteins

Author(s): Václav Brázda, Lucia Hároníková, Jack Liao, Miroslav Fojta
Published in: International Journal of Molecular Sciences, Issue 14220067, 2014, Page(s) 17493-17517, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms151017493

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation

Author(s): S. K. Mishra, M. Kara, M. Zacharias, J. Koca
Published in: Glycobiology, Issue 09596658, 2013, Page(s) 70-84, ISSN 0959-6658
Publisher: 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

Author(s): Kateřina Němcová, Peter Šebest, Luděk Havran, Petr Orság, Miroslav Fojta, Hana Pivoňková
Published in: Analytical and Bioanalytical Chemistry, Issue 16182642, 2014, Page(s) 5843-5852, ISSN 1618-2642
Publisher: Springer Verlag
DOI: 10.1007/s00216-014-7996-0

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

Author(s): Konstantinos Tripsianes, Nam K. Chu, Anders Friberg, Michael Sattler, Christian F. W. Becker
Published in: ACS Chemical Biology, Issue 15548929, 2014, Page(s) 347-352, ISSN 1554-8929
Publisher: American Chemical Society
DOI: 10.1021/cb400723j

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

Author(s): Pavel Kadeřávek, Vojtěch Zapletal, Alžbeta Rabatinová, Libor Krásný, Vladimír Sklenář, Lukáš Žídek
Published in: Journal of Biomolecular NMR, Issue 09252738, 2014, Page(s) 193-207, ISSN 0925-2738
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10858-014-9816-4

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

Author(s): Jitka Dadová, Petr Orság, Radek Pohl, Marie Brázdová, Miroslav Fojta, Michal Hocek
Published in: Angewandte Chemie International Edition, Issue 14337851, 2013, Page(s) 10515-10518, ISSN 1433-7851
Publisher: 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

Author(s): Daniel Nemecek, Pavel Plevka, Evzen Boura
Published in: The Protein Journal, Issue 15723887, 2013, Page(s) 635-640, ISSN 1572-3887
Publisher: 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

Author(s): Jan Vícha, Michael Patzschke, Radek Marek
Published in: Physical Chemistry Chemical Physics, Issue 14639076, 2013, Page(s) 7740, ISSN 1463-9076
Publisher: 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

Author(s): Ales Danhel, Veronika Raindlova, Ludek Havran, Jiri Barek, Michal Hocek, Miroslav Fojta
Published in: Electrochimica Acta, Issue 00134686, 2014, Page(s) 348-357, ISSN 0013-4686
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.electacta.2014.02.137

Instability restricts signaling of multiple fibroblast growth factors

Author(s): 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
Published in: Cellular and Molecular Life Sciences, Issue 1420682X, 2015, Page(s) 2445-2459, ISSN 1420-682X
Publisher: Birkhauser Verlag
DOI: 10.1007/s00018-015-1856-8

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

Author(s): K. Tripsianes, A. Friberg, C. Barrandon, M. Brooks, H. van Tilbeurgh, B. Seraphin, M. Sattler
Published in: Journal of Biological Chemistry, Issue 00219258, 2014, Page(s) 28640-28650, ISSN 0021-9258
Publisher: 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

Author(s): Zdeněk Kříž, Jiří Klusák, Zdena Krištofíková, Jaroslav Koča
Published in: PLoS ONE, Issue 19326203, 2013, Page(s) e62914, ISSN 1932-6203
Publisher: 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

Author(s): Jiří Nováček, Lubomír Janda, Radka Dopitová, Lukáš Žídek, Vladimír Sklenář
Published in: Journal of Biomolecular NMR, Issue 09252738, 2013, Page(s) 291-301, ISSN 0925-2738
Publisher: 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

Author(s): Ales Danhel, Veronika Raindlova, Ludek Havran, Hana Pivonkova, Michal Hocek, Miroslav Fojta
Published in: Electrochimica Acta, Issue 00134686, 2014, Page(s) 122-131, ISSN 0013-4686
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.electacta.2013.09.147

High-quality and universal empirical atomic charges for chemoinformatics applications

Author(s): Stanislav Geidl, Tomáš Bouchal, Tomáš Raček, Radka Svobodová Vařeková, Václav Hejret, Aleš Křenek, Ruben Abagyan, Jaroslav Koča
Published in: Journal of Cheminformatics, Issue 17582946, 2015, ISSN 1758-2946
Publisher: 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

Author(s): Cina Foroutan-Nejad, Radek Marek
Published in: Phys. Chem. Chem. Phys., Issue 14639076, 2014, Page(s) 2508-2514, ISSN 1463-9076
Publisher: 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

Author(s): Lukáš Fojt, Miroslav Fojta, Bohumír Grüner, Radim Vespalec
Published in: Journal of Electroanalytical Chemistry, Issue 15726657, 2013, Page(s) 38-42, ISSN 1572-6657
Publisher: Elsevier BV
DOI: 10.1016/j.jelechem.2013.08.016

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

Author(s): A. Nyarko, Y. Song, J. Novacek, L. Zidek, E. Barbar
Published in: Journal of Biological Chemistry, Issue 00219258, 2013, Page(s) 2614-2622, ISSN 0021-9258
Publisher: 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

Author(s): Helena Konvalinová, Zuzana Dvořáková, Daniel Renčiuk, Klára Bednářová, Iva Kejnovská, Lukáš Trantírek, Michaela Vorlíčková, Janos Sagi
Published in: Biochimie, Issue 03009084, 2015, Page(s) 15-25, ISSN 0300-9084
Publisher: Elsevier BV
DOI: 10.1016/j.biochi.2015.07.013

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

Author(s): Sophia Bazzi, Jan Novotný, Yevgen P. Yurenko, Radek Marek
Published in: Chemistry - A European Journal, Issue 09476539, 2015, Page(s) 9414-9425, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201500743

Expression of FGF19 in human embryonic stem cells

Author(s): Pavel Krejci, Michaela Kunova, Iva Kubikova, Lukas Trantirek, Alois Kozubik, Petr Dvorak
Published in: STEM CELLS, Issue 10665099, 2013, Page(s) 2582-2584, ISSN 1066-5099
Publisher: 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

Author(s): Pavlína Vidláková, Hana Pivoňková, Miroslav Fojta, Luděk Havran
Published in: Monatshefte für Chemie - Chemical Monthly, Issue 00269247, 2015, Page(s) 839-847, ISSN 0026-9247
Publisher: Springer Verlag
DOI: 10.1007/s00706-015-1435-6

Biophysical and electrochemical studies of protein–nucleic acid interactions

Author(s): Richard P. Bowater, Andrew M. Cobb, Hana Pivonkova, Ludek Havran, Miroslav Fojta
Published in: Monatshefte für Chemie - Chemical Monthly, Issue 00269247, 2015, Page(s) 723-739, ISSN 0026-9247
Publisher: 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

Author(s): Tomáš Trnka, Stanislav Kozmon, Igor Tvaroška, Jaroslav Koča
Published in: PLOS Computational Biology, Issue 1553734X, 2015, Page(s) e1004061, ISSN 1553-734X
Publisher: 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

Author(s): Jan Vícha, Cina Foroutan-Nejad, Tomasz Pawlak, Markéta L. Munzarová, Michal Straka, Radek Marek
Published in: Journal of Chemical Theory and Computation, Issue 15499618, 2015, Page(s) 1509-1517, ISSN 1549-9618
Publisher: 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

Author(s): Jiří Emmer, Andrea Vavrinská, Vladimír Sychrovský, Ladislav Benda, Zdeněk Kříž, Jaroslav Koča, Rolf Boelens, Vladimír Sklenář, Lukáš Trantírek
Published in: Journal of Biomolecular NMR, Issue 09252738, 2013, Page(s) 59-70, ISSN 0925-2738
Publisher: 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

Author(s): Peter Šebest, Marie Brázdová, Miroslav Fojta, Hana Pivoňková
Published in: International Journal of Molecular Sciences, Issue 14220067, 2015, Page(s) 3163-3177, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms16023163

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

Author(s): Petra Ménová, Hana Cahová, Medard Plucnara, Luděk Havran, Miroslav Fojta, Michal Hocek
Published in: Chemical Communications, Issue 13597345, 2013, Page(s) 4652, ISSN 1359-7345
Publisher: Royal Society of Chemistry
DOI: 10.1039/c3cc41438h

A novel variant of FGFR3 causes proportionate short stature

Author(s): 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
Published in: European Journal of Endocrinology, Issue 08044643, 2015, Page(s) 763-770, ISSN 0804-4643
Publisher: BioScientifica Ltd.
DOI: 10.1530/EJE-14-0945

In-Cell NMR and EPR Spectroscopy of Biomacromolecules

Author(s): Robert Hänsel, Laura M. Luh, Ivan Corbeski, Lukáš Trantirek, Volker Dötsch
Published in: Angewandte Chemie International Edition, Issue 14337851, 2014, Page(s) 10300-10314, ISSN 1433-7851
Publisher: 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

Author(s): Jitka Dadová, Pavlína Vidláková, Radek Pohl, Luděk Havran, Miroslav Fojta, Michal Hocek
Published in: The Journal of Organic Chemistry, Issue 00223263, 2013, Page(s) 9627-9637, ISSN 0022-3263
Publisher: American Chemical Society
DOI: 10.1021/jo4011574

Molecular Basis for Coordinating Transcription Termination with Noncoding RNA Degradation

Author(s): Agnieszka Tudek, Odil Porrua, Tomasz Kabzinski, Michael Lidschreiber, Karel Kubicek, Andrea Fortova, François Lacroute, Stepanka Vanacova, Patrick Cramer, Richard Stefl, Domenico Libri
Published in: Molecular Cell, Issue 10972765, 2014, Page(s) 467-481, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2014.05.031

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

Author(s): Manju Kumari, Stanislav Kozmon, Petr Kulhánek, Jakub Štepán, Igor Tvaroška, Jaroslav Koča
Published in: The Journal of Physical Chemistry B, Issue 15206106, 2015, Page(s) 4371-4381, ISSN 1520-6106
Publisher: American Chemical Society
DOI: 10.1021/jp511235f

Author(s): Pavel Kadeřávek, Sarina Grutsch, Nicola Salvi, Martin Tollinger, Lukáš Žídek, Geoffrey Bodenhausen, Fabien Ferrage
Published in: Journal of Biomolecular NMR, Issue 09252738, 2015, Page(s) 353-365, ISSN 0925-2738
Publisher: 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

Author(s): Veronika Papoušková, Pavel Kadeřávek, Olga Otrusinová, Alžbeta Rabatinová, Hana Šanderová, Jiří Nováček, Libor Krásný, Vladimír Sklenář, Lukáš Žídek
Published in: ChemBioChem, Issue 14394227, 2013, Page(s) 1772-1779, ISSN 1439-4227
Publisher: 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

Author(s): Jaromír Toušek, Michal Straka, Vladimír Sklenář, Radek Marek
Published in: The Journal of Physical Chemistry A, Issue 10895639, 2013, Page(s) 661-669, ISSN 1089-5639
Publisher: American Chemical Society
DOI: 10.1021/jp310470f

High-Resolution Insight into G-Overhang Architecture

Author(s): Robert Hänsel, Frank Löhr, Lukáš Trantirek, Volker Dötsch
Published in: Journal of the American Chemical Society, Issue 00027863, 2013, Page(s) 2816-2824, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/ja312403b

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

Author(s): R. S. Va ekova, D. Jaiswal, D. Sehnal, C.-M. Ionescu, S. Geidl, L. Pravda, V. Horsky, M. Wimmerova, J. Ko a
Published in: Nucleic Acids Research, Issue 03051048, 2014, Page(s) W227-W233, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gku426

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

Author(s): Josef Houser, Jan Komarek, Gianluca Cioci, Annabelle Varrot, Anne Imberty, Michaela Wimmerova
Published in: Acta Crystallographica Section D Biological Crystallography, Issue 13990047, 2015, Page(s) 442-453, ISSN 1399-0047
Publisher: 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

Author(s): A. Rabatinova, H. Sanderova, J. Jirat Matejckova, J. Korelusova, L. Sojka, I. Barvik, V. Papouskova, V. Sklenar, L. Zidek, L. Krasny
Published in: Journal of Bacteriology, Issue 00219193, 2013, Page(s) 2603-2611, ISSN 0021-9193
Publisher: 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

Author(s): Petr Stadlbauer, Petra Kührová, Pavel Banáš, Jaroslav Koča, Giovanni Bussi, Lukáš Trantírek, Michal Otyepka, Jiří Šponer
Published in: Nucleic Acids Research, Issue 03051048, 2015, Page(s) gkv994, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkv994

Extended molecular dynamics of a c-kit promoter quadruplex

Author(s): Barira Islam, Petr Stadlbauer, Miroslav Krepl, Jaroslav Koca, Stephen Neidle, Shozeb Haider, Jiri Sponer
Published in: Nucleic Acids Research, Issue 03051048, 2015, Page(s) 8673-8693, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkv785

New sensitive detection method for lectin hemagglutination using microscopy

Author(s): Lenka Adamová, Lenka Malinovská, Michaela Wimmerová
Published in: Microscopy Research and Technique, Issue 1059910X, 2014, Page(s) 841-849, ISSN 1059-910X
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/jemt.22407

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

Author(s): D. Ustianenko, D. Hrossova, D. Potesil, K. Chalupnikova, K. Hrazdilova, J. Pachernik, K. Cetkovska, S. Uldrijan, Z. Zdrahal, S. Vanacova
Published in: RNA, Issue 13558382, 2013, Page(s) 1632-1638, ISSN 1355-8382
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1261/rna.040055.113

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

Author(s): Zdeněk Kříž, Jan Adam, Jana Mrázková, Petros Zotos, Thomais Chatzipavlou, Michaela Wimmerová, Jaroslav Koča
Published in: Journal of Computer-Aided Molecular Design, Issue 0920654X, 2014, Page(s) 951-960, ISSN 0920-654X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10822-014-9774-7

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

Author(s): Shivaji S. Kadam, Lukáš Maier, Tomáš Šolomek, Marek Nečas, Karel Šmejkal, Jiří Dostál, Vladimír Sklenář, Radek Marek
Published in: Journal of Physical Organic Chemistry, Issue 08943230, 2013, Page(s) 814-821, ISSN 0894-3230
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/poc.3175

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

Author(s): 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
Published in: PLOS ONE, Issue 19326203, 2015, Page(s) e0119899, ISSN 1932-6203
Publisher: 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

Author(s): Marie Brázdová, Lucie Navrátilová, Vlastimil Tichý, Kateřina Němcová, Matej Lexa, Roman Hrstka, Petr Pečinka, Matej Adámik, Borivoj Vojtesek, Emil Paleček, Wolfgang Deppert, Miroslav Fojta
Published in: PLoS ONE, Issue 19326203, 2013, Page(s) e59567, ISSN 1932-6203
Publisher: 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?

Author(s): Stanislav Geidl, Radka Svobodová Vařeková, Veronika Bendová, Lukáš Petrusek, Crina-Maria Ionescu, Zdeněk Jurka, Ruben Abagyan, Jaroslav Koča
Published in: Journal of Chemical Information and Modeling, Issue 15499596, 2015, Page(s) 1088-1097, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/ci500758w

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

Author(s): Jitka Dadová, Milan Vrábel, Matej Adámik, Marie Brázdová, Radek Pohl, Miroslav Fojta, Michal Hocek
Published in: Chemistry - A European Journal, Issue 09476539, 2015, Page(s) 16091-16102, ISSN 0947-6539
Publisher: 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

Author(s): Igor Tvaroška, Stanislav Kozmon, Michaela Wimmerová, Jaroslav Koča
Published in: Chemistry - A European Journal, Issue 09476539, 2013, Page(s) 8153-8162, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201300383

Tailoring the properties of quadruplex nucleobases for biological and nanomaterial applications

Author(s): Jan Novotný, Yevgen P. Yurenko, Petr Kulhánek, Radek Marek
Published in: Physical Chemistry Chemical Physics, Issue 14639076, 2014, Page(s) 15241, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/c4cp00541d

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

Author(s): Crina-Maria Ionescu, David Sehnal, Francesco L. Falginella, Purbaj Pant, Lukáš Pravda, Tomáš Bouchal, Radka Svobodová Vařeková, Stanislav Geidl, Jaroslav Koča
Published in: Journal of Cheminformatics, Issue 17582946, 2015, ISSN 1758-2946
Publisher: 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

Author(s): Cina Foroutan-Nejad, Shant Shahbazian, Radek Marek
Published in: Chemistry - A European Journal, Issue 09476539, 2014, Page(s) 10140-10152, ISSN 0947-6539
Publisher: 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

Author(s): J. Vym tal, S. R. Bathula, J. erny, R. Chaloupkova, L. idek, V. Sklena , J. Vondra ek
Published in: Protein Engineering Design and Selection, Issue 17410126, 2014, Page(s) 463-472, ISSN 1741-0126
Publisher: Oxford University Press
DOI: 10.1093/protein/gzu046

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

Author(s): Cina Foroutan-Nejad, Zahra Badri, Radek Marek
Published in: Phys. Chem. Chem. Phys., Issue 14639076, 2015, Page(s) 30670-30679, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/c5cp05777a

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

Author(s): Tomasz Pawlak, Daria Niedzielska, Jan Vícha, Radek Marek, Leszek Pazderski
Published in: Journal of Organometallic Chemistry, Issue 0022328X, 2014, Page(s) 58-66, ISSN 0022-328X
Publisher: 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

Author(s): Sushil K. Mishra, Gaetano Calabró, Hannes H. Loeffler, Julien Michel, Jaroslav Koča
Published in: Journal of Chemical Theory and Computation, Issue 15499618, 2015, Page(s) 3333-3345, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.5b00159

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

Author(s): Shivaji S. Kadam, Lukáš Maier, Ioannis Kostakis, Nicole Pouli, Jaromír Toušek, Marek Nečas, Panagiotis Marakos, Radek Marek
Published in: European Journal of Organic Chemistry, Issue 1434193X, 2013, Page(s) 6811-6822, ISSN 1434-193X
Publisher: 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

Author(s): Kateřina Bouzková, Martin Babinský, Lucie Novosadová, Radek Marek
Published in: Journal of Chemical Theory and Computation, Issue 15499618, 2013, Page(s) 2629-2638, ISSN 1549-9618
Publisher: 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

Author(s): Michal Rouchal, Alena Matelová, Fabiana Pires de Carvalho, Robert Bernat, Dragan Grbić, Ivo Kuřitka, Martin Babinský, Radek Marek, Richard Čmelík, Robert Vícha
Published in: Supramolecular Chemistry, Issue 10610278, 2013, Page(s) 349-361, ISSN 1061-0278
Publisher: 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

Author(s): Jana Balintová, Medard Plucnara, Pavlína Vidláková, Radek Pohl, Luděk Havran, Miroslav Fojta, Michal Hocek
Published in: Chemistry - A European Journal, Issue 09476539, 2013, Page(s) 12720-12731, ISSN 0947-6539
Publisher: 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

Author(s): O. Bernatik, K. edova, C. Schille, R. S. Ganji, I. ervenka, L. Trantirek, A. Schambony, Z. Zdrahal, V. Bryja
Published in: Journal of Biological Chemistry, Issue 00219258, 2014, Page(s) 23520-23533, ISSN 0021-9258
Publisher: 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

Author(s): Diana C. Rodriguez Camargo, Konstantinos Tripsianes, Tobias G. Kapp, Joaquim Mendes, Jasmin Schubert, Burghard Cordes, Bernd Reif
Published in: Protein Expression and Purification, Issue 10465928, 2015, Page(s) 49-56, ISSN 1046-5928
Publisher: 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

Author(s): Lukáš Fojt, Miroslav Fojta, Bohumír Grüner, Radim Vespalec
Published in: Journal of Electroanalytical Chemistry, Issue 15726657, 2014, Page(s) 16-19, ISSN 1572-6657
Publisher: Elsevier BV
DOI: 10.1016/j.jelechem.2014.07.023

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

Author(s): Gabriel Demo, Barbora Fliedrová, Lenka Weignerová, Michaela Wimmerová
Published in: Acta Crystallographica Section F Structural Biology and Crystallization Communications, Issue 17443091, 2013, Page(s) 288-291, ISSN 1744-3091
Publisher: International Union of Crystallography
DOI: 10.1107/S1744309113002522

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

Author(s): M. Babinsky, R. Fiala, I. Kejnovska, K. Bedna ova, R. Marek, J. Sagi, V. Sklena , M. Vorli kova
Published in: Nucleic Acids Research, Issue 03051048, 2014, Page(s) 14031-14041, ISSN 0305-1048
Publisher: 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

Author(s): Jan Vícha, Michal Straka, Markéta L. Munzarová, Radek Marek
Published in: Journal of Chemical Theory and Computation, Issue 15499618, 2014, Page(s) 1489-1499, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/ct400726y

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

Author(s): Martin Obr, Romana Hadravová, Michal Doležal, Ivana Křžová, Veronika Papoušková, Lukáš Žídek, Richard Hrabal, Tomáš Ruml, Michaela Rumlová
Published in: Retrovirology, Issue 17424690, 2014, ISSN 1742-4690
Publisher: 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

Author(s): Cina Foroutan-Nejad, Jan Vícha, Radek Marek, Michael Patzschke, Michal Straka
Published in: Phys. Chem. Chem. Phys., Issue 14639076, 2015, Page(s) 24182-24192, ISSN 1463-9076
Publisher: 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

Author(s): Stanislav Standara, Petr Kulhánek, Radek Marek, Michal Straka
Published in: Journal of Computational Chemistry, Issue 01928651, 2013, Page(s) 1890-1898, ISSN 0192-8651
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/jcc.23334

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

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

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

Author(s): R. G. Valencia, G. Walko, L. Janda, J. Novacek, E. Mihailovska, S. Reipert, K. Andra-Marobela, G. Wiche
Published in: Molecular Biology of the Cell, Issue 10591524, 2013, Page(s) 768-784, ISSN 1059-1524
Publisher: American Society for Cell Biology
DOI: 10.1091/mbc.E12-06-0488

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

Author(s): Zahra Badri, Shubhrodeep Pathak, Heike Fliegl, Parviz Rashidi-Ranjbar, Radovan Bast, Radek Marek, Cina Foroutan-Nejad, Kenneth Ruud
Published in: Journal of Chemical Theory and Computation, Issue 15499618, 2013, Page(s) 4789-4796, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/ct4007184

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

Author(s): Zaiyong Zhang, Justin Porter, Konstantinos Tripsianes, Oliver F. Lange
Published in: Journal of Biomolecular NMR, Issue 09252738, 2014, Page(s) 135-145, ISSN 0925-2738
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10858-014-9832-4

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

Author(s): G. Demo, V. Horska, B. Fliedrova, J. t pan, J. Ko a, L. Weignerova, V. K en, M. Wimmerova
Published in: Glycobiology, Issue 09596658, 2014, Page(s) 1301-1311, ISSN 0959-6658
Publisher: Oxford University Press
DOI: 10.1093/glycob/cwu074

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

Author(s): Gabriel Demo, Veronika Papoušková, Jan Komárek, Pavel Kadeřávek, Olga Otrusinová, Pavel Srb, Alžbeta Rabatinová, Libor Krásný, Lukáš Žídek, Vladimír Sklenář, Michaela Wimmerová
Published in: Journal of Structural Biology, Issue 10478477, 2014, Page(s) 174-186, ISSN 1047-8477
Publisher: 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

Author(s): 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
Published in: PLoS ONE, Issue 19326203, 2013, Page(s) e83077, ISSN 1932-6203
Publisher: 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

Author(s): Jiří Červeň, Luděk Havran, Petr Pečinka, Miroslav Fojta
Published in: Electroanalysis, Issue 10400397, 2015, Page(s) 2268-2271, ISSN 1040-0397
Publisher: 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

Author(s): Lucia Hároníková, Jan Špaček, Medard Plucnara, Petra Horáková, Hana Pivoňková, Luděk Havran, Arzum Erdem, Miroslav Fojta
Published in: Monatshefte für Chemie - Chemical Monthly, Issue 00269247, 2015, Page(s) 849-855, ISSN 0026-9247
Publisher: 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

Author(s): Oksana Degtjarik, Radka Dopitova, Sandra Puehringer, Eliska Nejedla, Michal Kuty, Manfred S. Weiss, Jan Hejatko, Lubomir Janda, Ivana Kuta Smatanova
Published in: Acta Crystallographica Section F Structural Biology and Crystallization Communications, Issue 17443091, 2013, Page(s) 158-161, ISSN 1744-3091
Publisher: 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

Author(s): Konstantinos Gkionis, Holger Kruse, James A. Platts, Arnošt Mládek, Jaroslav Koča, Jiří Šponer
Published in: Journal of Chemical Theory and Computation, Issue 15499618, 2014, Page(s) 1326-1340, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/ct4009969

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

Author(s): Yevgen P. Yurenko, Jan Novotný, Mariusz P. Mitoraj, Vladimir Sklenář, Artur Michalak, Radek Marek
Published in: Journal of Chemical Theory and Computation, Issue 15499618, 2014, Page(s) 5353-5365, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/ct5007554

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

Author(s): P. kolakova, S. Foldynova-Trantirkova, K. Bedna ova, R. Fiala, M. Vorli kova, L. Trantirek
Published in: Nucleic Acids Research, Issue 03051048, 2015, Page(s) 4733-4745, ISSN 0305-1048
Publisher: 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

Author(s): Zahra Badri, Kateřina Bouzková, Cina Foroutan-Nejad, Radek Marek
Published in: Crystal Growth & Design, Issue 15287483, 2014, Page(s) 2763-2772, ISSN 1528-7483
Publisher: 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

Author(s): Yevgen P. Yurenko, Jan Novotný, Vladimir Sklenář, Radek Marek
Published in: Phys. Chem. Chem. Phys., Issue 14639076, 2014, Page(s) 2072-2084, ISSN 1463-9076
Publisher: 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

Author(s): Pavlína Vidláková, Hana Pivoňková, Iva Kejnovská, Libuše Trnková, Michaela Vorlíčková, Miroslav Fojta, Luděk Havran
Published in: Analytical and Bioanalytical Chemistry, Issue 16182642, 2015, Page(s) 5817-5826, ISSN 1618-2642
Publisher: 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

Author(s): Noam Y. Haba, Renana Gross, Jiri Novacek, Hadassa Shaked, Lukas Zidek, Mira Barda-Saad, Jordan H. Chill
Published in: Biophysical Journal, Issue 00063495, 2013, Page(s) 481-493, ISSN 0006-3495
Publisher: 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

Author(s): Gulsah Congur, Medard Plucnara, Arzum Erdem, Miroslav Fojta
Published in: Electroanalysis, Issue 10400397, 2015, Page(s) 1579-1586, ISSN 1040-0397
Publisher: 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

Author(s): Jana Balintová, Jan Špaček, Radek Pohl, Marie Brázdová, Luděk Havran, Miroslav Fojta, Michal Hocek
Published in: Chem. Sci., Issue 20416520, 2015, Page(s) 575-587, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/c4sc01906g

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

Author(s): David Sehnal, Radka Svobodová Vařeková, Karel Berka, Lukáš Pravda, Veronika Navrátilová, Pavel Banáš, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koča
Published in: Journal of Cheminformatics, Issue 17582946, 2013, Page(s) 39, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/1758-2946-5-39

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

Author(s): Petr Stadlbauer, Lukáš Trantírek, Thomas E. Cheatham, Jaroslav Koča, Jiří Šponer
Published in: Biochimie, Issue 03009084, 2014, Page(s) 22-35, ISSN 0300-9084
Publisher: Elsevier BV
DOI: 10.1016/j.biochi.2014.07.009

Anatomy of enzyme channels

Author(s): Lukáš Pravda, Karel Berka, Radka Svobodová Vařeková, David Sehnal, Pavel Banáš, Roman A Laskowski, Jaroslav Koča, Michal Otyepka
Published in: BMC Bioinformatics, Issue 14712105, 2014, ISSN 1471-2105
Publisher: 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

Author(s): Petra Borkovcová, Blanka Pekárová, Martina Válková, Radka Dopitová, Břetislav Brzobohatý, Lubomír Janda, Jan Hejátko
Published in: Phytochemistry, Issue 00319422, 2014, Page(s) 6-15, ISSN 0031-9422
Publisher: 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

Author(s): Jakub Šebera, Lukáš Trantírek, Yoshiyuki Tanaka, Radim Nencka, Jiří Fukal, Vladimír Sychrovský
Published in: RSC Adv., Issue 20462069, 2014, Page(s) 44043-44051, ISSN 2046-2069
Publisher: Royal Society of Chemistry
DOI: 10.1039/c4ra08278h

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

Author(s): Vojtěch Kubáň, Jiří Nováček, Ladislav Bumba, Lukáš Žídek
Published in: Biomolecular NMR Assignments, Issue 18742718, 2015, Page(s) 435-440, ISSN 1874-2718
Publisher: 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

Author(s): Jan Vícha, Jan Novotný, Michal Straka, Michal Repisky, Kenneth Ruud, Stanislav Komorovsky, Radek Marek
Published in: Phys. Chem. Chem. Phys., Issue 14639076, 2015, Page(s) 24944-24955, ISSN 1463-9076
Publisher: 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

Author(s): Y. Liu, H. K. Salter, A. N. Holding, C. M. Johnson, E. Stephens, P. J. Lukavsky, J. Walshaw, S. L. Bullock
Published in: Genes & Development, Issue 08909369, 2013, Page(s) 1233-1246, ISSN 0890-9369
Publisher: 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

Author(s): Martin Babinský, Kateřina Bouzková, Matej Pipíška, Lucie Novosadová, Radek Marek
Published in: The Journal of Physical Chemistry A, Issue 10895639, 2013, Page(s) 497-503, ISSN 1089-5639
Publisher: American Chemical Society
DOI: 10.1021/jp310967b

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

Author(s): Crina-Maria Ionescu, Stanislav Geidl, Radka Svobodová Vařeková, Jaroslav Koča
Published in: Journal of Chemical Information and Modeling, Issue 15499596, 2013, Page(s) 2548-2558, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/ci400448n

Fluorescent Cellular Assay for Screening Agents Inhibiting Pseudomonas aeruginosa Adherence

Author(s): Libuše Nosková, Božena Kubíčková, Lucie Vašková, Barbora Bláhová, Michaela Wimmerová, Marie Stiborová, Petr Hodek
Published in: Sensors, Issue 14248220, 2015, Page(s) 1945-1953, ISSN 1424-8220
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/s150101945

Methoxyphenol and Dihydrobenzofuran as Oxidizable Labels for Electrochemical Detection of DNA

Author(s): Anna Simonova, Jana Balintová, Radek Pohl, Luděk Havran, Miroslav Fojta, Michal Hocek
Published in: ChemPlusChem, Issue 21926506, 2014, Page(s) n/a-n/a, ISSN 2192-6506
Publisher: Wiley-VCH Verlag
DOI: 10.1002/cplu.201402194

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

Author(s): David Sehnal, Lukáš Pravda, Radka Svobodová Vařeková, Crina-Maria Ionescu, Jaroslav Koča
Published in: Nucleic Acids Research, Issue 03051048, 2015, Page(s) W383-W388, ISSN 0305-1048
Publisher: 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

Author(s): D. Sehnal, R. Svobodova Va ekova, L. Pravda, C.-M. Ionescu, S. Geidl, V. Horsky, D. Jaiswal, M. Wimmerova, J. Ko a
Published in: Nucleic Acids Research, Issue 03051048, 2015, Page(s) D369-D375, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gku1118

Toward optimal-resolution NMR of intrinsically disordered proteins

Author(s): Jiří Nováček, Lukáš Žídek, Vladimír Sklenář
Published in: Journal of Magnetic Resonance, Issue 10907807, 2014, Page(s) 41-52, ISSN 1090-7807
Publisher: Academic Press
DOI: 10.1016/j.jmr.2013.12.008

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

Author(s): Carolina Estarellas, Michal Otyepka, Jaroslav Koča, Pavel Banáš, Miroslav Krepl, Jiří Šponer
Published in: Biochimica et Biophysica Acta (BBA) - General Subjects, Issue 03044165, 2015, Page(s) 1072-1090, ISSN 0304-4165
Publisher: 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

Author(s): D. Hrossova, T. Sikorsky, D. Potesil, M. Bartosovic, J. Pasulka, Z. Zdrahal, R. Stefl, S. Vanacova
Published in: Nucleic Acids Research, Issue 03051048, 2015, Page(s) 4236-4248, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkv240

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

Author(s): Cina Foroutan-Nejad, Jan Vicha, Radek Marek
Published in: Chemistry - A European Journal, Issue 09476539, 2014, Page(s) 11584-11590, ISSN 0947-6539
Publisher: 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

Author(s): Yevgen P. Yurenko, Jan Novotný, Vladimir Sklenář, Radek Marek
Published in: Chemistry - A European Journal, Issue 09476539, 2015, Page(s) 17933-17943, ISSN 0947-6539
Publisher: 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

Author(s): Mainak Debnath, Arpan Dutta, Surajit Biswas, Kalyan Kumar Das, Hon Man Lee, Jan Vícha, Radek Marek, Jaromir Marek, Mahammad Ali
Published in: Polyhedron, Issue 02775387, 2013, Page(s) 189-198, ISSN 0277-5387
Publisher: Pergamon Press
DOI: 10.1016/j.poly.2013.07.013

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

Author(s): Matej Zábrady, Vendula Hrdinová, Bruno Müller, Udo Conrad, Jan Hejátko, Lubomír Janda
Published in: PLoS ONE, Issue 19326203, 2014, Page(s) e109875, ISSN 1932-6203
Publisher: Public Library of Science
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Predicting p Ka values from EEM atomic charges

Author(s): Radka Vařeková, Stanislav Geidl, Crina-Maria Ionescu, Ondřej Skřehota, Tomáš Bouchal, David Sehnal, Ruben Abagyan, Jaroslav Koča
Published in: Journal of Cheminformatics, Issue 17582946, 2013, Page(s) 18, ISSN 1758-2946
Publisher: Chemistry Central
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On the non-classical contribution in lone-pair–π interaction: IQA perspective

Author(s): Zahra Badri, Cina Foroutan-Nejad, Jiri Kozelka, Radek Marek
Published in: Phys. Chem. Chem. Phys., Issue 14639076, 2015, Page(s) 26183-26190, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/c5cp04489h

Enzyme-linked electrochemical DNA ligation assay using magnetic beads

Author(s): Eva Stejskalová, Petra Horáková, Jan Vacek, Richard P. Bowater, Miroslav Fojta
Published in: Analytical and Bioanalytical Chemistry, Issue 16182642, 2014, Page(s) 4129-4136, ISSN 1618-2642
Publisher: Springer Verlag
DOI: 10.1007/s00216-014-7811-y

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