Personal information

Emails & domains

Verified email domains

Websites & social links

Please see my website bs.structbio.org

Other IDs

ResearcherID: D-2565-2009

Keywords

DNA structure, DNA dynamics, protein engineering, structural bioinformatics

Countries

Czech Republic

Biography

I study structure and recognition of DNA, RNA, and proteins by bioinformatics and biophysics. Please see my web bs.structbio.org for more details.

Activities

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Employment (1)

ASCR, Institute of Biotechnology: Vestec, Prague region, CZ

2008-05-02 to present | Director of the institute, Head of laboratory (Laboratory of Biomolecular Recognition)
Employment
Source: Self-asserted source
Bohdan Schneider

Education and qualifications (1)

Prague Institute of Chemical Technology: Prague, CZ

1977 to 1982 | Ms. (Physical chemistry)
Education
Source: Self-asserted source
Bohdan Schneider

Works (50 of 103)

Items per page:
Page 1 of 3

Increasing recombinant protein production in E. coli via FACS‐based selection of N‐terminal coding DNA libraries

The FEBS Journal
2025-03 | Journal article
DOI: 10.1111/febs.17376
Contributors: Štěpán Herynek; Jakub Svoboda; Maroš Huličiak; Yoav Peleg; Ľubica Škultétyová; Pavel Mikulecký; Bohdan Schneider
Source: check_circle
Crossref

Light-dependent flavin redox and adduct states control the conformation and DNA-binding activity of the transcription factor EL222

Nucleic Acids Research
2025-03-20 | Journal article
DOI: 10.1093/nar/gkaf215
Contributors: Aditya S Chaudhari; Adrien Favier; Zahra Aliakbar Tehrani; Tomáš Kovaľ; Inger Andersson; Bohdan Schneider; Jan Dohnálek; Jiří Černý; Bernhard Brutscher; Gustavo Fuertes
Source: check_circle
Crossref

Light-dependent flavin redox and adduct states control the conformation and DNA binding activity of the transcription factor EL222

2024-11-06 | Preprint
DOI: 10.1101/2024.11.06.618433
Contributors: Aditya S. Chaudhari; Adrien Favier; Zahra Aliakbar Tehrani; Tomáš Kovaľ; Inger Andersson; Bohdan Schneider; Jan Dohnálek; Jiří Černý; Bernhard Brutscher; Gustavo Fuertes
Source: check_circle
Crossref

When will RNA get its AlphaFold moment?

Nucleic Acids Research
2023-10-13 | Journal article
DOI: 10.1093/nar/gkad726
Contributors: Bohdan Schneider; Blake Alexander Sweeney; Alex Bateman; Jiri Cerny; Tomasz Zok; Marta Szachniuk
Source: check_circle
Crossref

Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10

Journal of Applied Crystallography
2023-08-01 | Journal article
DOI: 10.1107/S160057672300479X
Contributors: Petr Kolenko; Pavel Mikulecký; Phuong Ngoc Pham; Martin Malý; Bohdan Schneider
Source: check_circle
Crossref

Conformation-based refinement of 18-mer DNA structures

Acta Crystallographica Section D Structural Biology
2023-07-01 | Journal article
DOI: 10.1107/S2059798323004679
Contributors: Jakub Svoboda; Daniel Berdár; Petr Kolenko; Jiří Černý; Zora Nováková; Jiří Pavlíček; Bohdan Schneider
Source: check_circle
Crossref

Combined in vitro and cell‐based selection display method producing specific binders against IL‐9 receptor in high yields

The FEBS Journal
2023-06 | Journal article
DOI: 10.1111/febs.16726
Contributors: Maroš Huličiak; Lada Biedermanová; Daniel Berdár; Štěpán Herynek; Lucie Kolářová; Jakub Tomala; Pavel Mikulecký; Bohdan Schneider
Source: check_circle
Crossref

Genetically encoded non‐canonical amino acids reveal asynchronous dark reversion of chromophore, backbone, and side‐chains in EL222

Protein Science
2023-04 | Journal article
DOI: 10.1002/pro.4590
Contributors: Aditya S. Chaudhari; Aditi Chatterjee; Catarina A. O. Domingos; Prokopis C. Andrikopoulos; Yingliang Liu; Inger Andersson; Bohdan Schneider; Víctor A. Lórenz‐Fonfría; Gustavo Fuertes
Source: check_circle
Crossref

Sub-Millisecond Photoinduced Dynamics of Free and EL222-Bound FMN by Stimulated Raman and Visible Absorption Spectroscopies

Biomolecules
2023-01-12 | Journal article
DOI: 10.3390/biom13010161
Contributors: Yingliang Liu; Aditya S. Chaudhari; Aditi Chatterjee; Prokopis C. Andrikopoulos; Alessandra Picchiotti; Mateusz Rebarz; Miroslav Kloz; Victor A. Lorenz-Fonfria; Bohdan Schneider; Gustavo Fuertes
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222

2022-09-17 | Preprint
DOI: 10.1101/2022.09.16.506679
Contributors: Aditya S. Chaudhari; Aditi Chatterjee; Catarina A.O. Domingos; Prokopis C. Andrikopoulos; Yingliang Liu; Inger Andersson; Bohdan Schneider; Víctor A. Lórenz-Fonfría; Gustavo Fuertes
Source: check_circle
Crossref

Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks

Acta Crystallographica Section D Structural Biology
2022-08-01 | Journal article
DOI: 10.1107/S2059798322006234
Contributors: Lada Biedermannová; Jiří Černý; Michal Malý; Michaela Nekardová; Bohdan Schneider
Source: check_circle
Crossref

De novo developed protein binders mimicking Interferon lambda signaling

The FEBS Journal
2022-05 | Journal article
DOI: 10.1111/febs.16300
Contributors: Lucie Kolářová; Jiří Zahradník; Maroš Huličiak; Pavel Mikulecký; Yoav Peleg; Maya Shemesh; Gideon Schreiber; Bohdan Schneider
Source: check_circle
Crossref

QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors

Physical Chemistry Chemical Physics
2021 | Journal article
DOI: 10.1039/D1CP00447F
Contributors: Prokopis C. Andrikopoulos; Aditya S. Chaudhari; Yingliang Liu; Patrick E. Konold; John T. M. Kennis; Bohdan Schneider; Gustavo Fuertes
Source: check_circle
Crossref

Protein Binder (ProBi) as a New Class of Structurally Robust Non-Antibody Protein Scaffold for Directed Evolution

Viruses
2021-01 | Journal article | Author
DOI: 10.3390/v13020190
Contributors: Phuong Ngoc Pham; Maroš Huličiak; Lada Biedermannová; Jiří Černý; Tatsiana Charnavets; Gustavo Fuertes; Štěpán Herynek; Lucie Kolářová; Petr Kolenko; Jiří Pavlíček et al.
Source: check_circle
Multidisciplinary Digital Publishing Institute

Femtosecond-to-nanosecond dynamics of flavin mononucleotide monitored by stimulated Raman spectroscopy and simulations

Physical Chemistry Chemical Physics
2020 | Journal article
DOI: 10.1039/c9cp04918e
Part of ISSN: 1463-9076
Part of ISSN: 1463-9084
Source: Self-asserted source
Bohdan Schneider

Demonstration of electron diffraction from membrane protein crystals grown in a lipidic mesophase after lamella preparation by focused ion beam milling at cryogenic temperatures

Journal of Applied Crystallography
2020-12-01 | Journal article
DOI: 10.1107/s1600576720013096
Part of ISSN: 1600-5767
Source: Self-asserted source
Bohdan Schneider

Structural variability of CG-rich DNA 18-mers accommodating double T–T mismatches

Acta Crystallographica Section D Structural Biology
2020-12-01 | Journal article
DOI: 10.1107/S2059798320014151
Contributors: Petr Kolenko; Jakub Svoboda; Jiří Černý; Tatsiana Charnavets; Bohdan Schneider
Source: check_circle
Crossref

Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org

Acta Crystallographica Section D Structural Biology
2020-09-01 | Journal article
DOI: 10.1107/S2059798320009389
Contributors: Jiří Černý; Paulína Božíková; Michal Malý; Michal Tykač; Lada Biedermannová; Bohdan Schneider
Source: check_circle
Crossref

A unified dinucleotide alphabet describing both RNA and DNA structures

Nucleic Acids Research
2020-06-19 | Journal article
DOI: 10.1093/nar/gkaa383
Contributors: Jiří Černý; Paulína Božíková; Jakub Svoboda; Bohdan Schneider
Source: check_circle
Crossref

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) [version 1; peer review: 1 approved, 3 approved with reservations]

2020-04-22 | Journal article
DOI: 10.12688/f1000research.20559.1
Part of ISSN: 2046-1402
Contributors: Christine Orengo; Sameer Velankar; Shoshana Wodak; Vincent Zoete; Alexandre M.J.J. Bonvin; Arne Elofsson; K. Anton Feenstra; Dietland L. Gerloff; Thomas Hamelryck; John M. Hancock et al.
Source: check_circle
F1000

Flexible regions govern promiscuous binding of IL‐24 to receptors IL‐20R1 and IL‐22R1

The FEBS Journal
2019-10 | Journal article
DOI: 10.1111/febs.14945
Contributors: Jiří Zahradník; Lucie Kolářová; Yoav Peleg; Petr Kolenko; Silvie Svidenská; Tatsiana Charnavets; Tamar Unger; Joel L. Sussman; Bohdan Schneider
Source: check_circle
Crossref

Interferons type II and their receptors R1 and R2 in fish species: Evolution, structure, and function

Fish & Shellfish Immunology
2018-08 | Journal article
DOI: 10.1016/j.fsi.2018.05.008
Contributors: Jiří Zahradník; Lucie Kolářová; Hana Pařízková; Petr Kolenko; Bohdan Schneider
Source: check_circle
Crossref

A DNA structural alphabet provides new insight into DNA flexibility

Acta Crystallographica Section D Structural Biology
2018-01-01 | Journal article
DOI: 10.1107/S2059798318000050
Contributors: Bohdan Schneider; Paulína Božíková; Iva Nečasová; Petr Čech; Daniel Svozil; Jiří Černý
Source: check_circle
Crossref

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations

Physical Chemistry Chemical Physics
2017 | Journal article
DOI: 10.1039/C7CP00187H
Contributors: Jiří Černý; Bohdan Schneider; Lada Biedermannová
Source: check_circle
Crossref

A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle

Genes
2017-10 | Journal article
DOI: 10.3390/genes8100278
Source: check_circle
Multidisciplinary Digital Publishing Institute
grade
Preferred source (of 2)‎

DNATCO: assignment of DNA conformers at dnatco.org

Nucleic Acids Res
2016 | Journal article
DOI: 10.1093/nar/gkw381
Contributors: Černý, J.; Božíková, P.; Schneider, B.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Hydration of proteins and nucleic acids: Advances in experiment and theory. A review

Biochim Biophys Acta
2016 | Journal article
DOI: 10.1016/j.bbagen.2016.05.036
Contributors: Biedermannová, L.; Schneider, B.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Conformational diversity of single-stranded DNA from bacterial repetitive extragenic palindromes: Implications for the DNA recognition elements of transposases

Biopolymers
2015 | Journal article
DOI: 10.1002/bip.22666
Contributors: Charnavets, T.; Nunvar, J.; Nečasová, I.; Völker, J.; Breslauer, K. J.; Schneider, B.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Monitoring RAYT activity by surface plasmon resonance biosensor

Anal Bioanal Chem
2015 | Journal article
DOI: 10.1007/s00216-015-8491-y
Contributors: Bocková, M.; Špringer, T.; Nečasová, I.; Nunvar, J.; Schneider, B.; Homola, J.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Redesigning Protein Cavities as a Strategy for Increasing Affinity in Protein-Protein Interaction: Interferon-𝛾 Receptor 1 as a Model

BioMed Research International
2015 | Journal article
DOI: 10.1155/2015/716945
Source: Self-asserted source
Bohdan Schneider
grade
Preferred source (of 2)‎

Bioinformatic analysis of the protein/DNA interface

Nucleic Acids Research
2014 | Journal article
DOI: 10.1093/nar/gkt1273
WOSUID:

WOS:000333093600053
Contributors: Schneider, B.; Cerny, J.; Svozil, D.; Cech, P.; Gelly, J. C.; de Brevern, A. G.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Draft Genome Sequence of Stenotrophomonas maltophilia Strain 5BA-I-2, a Soil Isolate and a Member of a Phylogenetically Basal Lineage

Genome Announc
2014 | Journal article
DOI: 10.1128/genomeA.00134-14
Contributors: Nunvar, J.; Elhottova, D.; Chronakova, A.; Schneider, B.; Licha, I.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Human interleukin-23 receptor antagonists derived from an albumin-binding domain scaffold inhibit IL-23-dependent ex vivo expansion of IL-17-producing T-cells

Proteins-Structure Function and Bioinformatics
2014 | Journal article
DOI: 10.1002/prot.24472
WOSUID:

WOS:000335955300009
Contributors: Kuchar, M.; Vankova, L.; Petrokova, H.; Cerny, J.; Osicka, R.; Pelak, O.; Sipova, H.; Schneider, B.; Homola, J.; Sebo, P. et al.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Local dynamics of proteins and DNA evaluated from crystallographic B factors

Acta Crystallographica Section D-Biological Crystallography
2014 | Journal article
DOI: 10.1107/S1399004714014631
WOSUID:

WOS:000341819500016
Contributors: Schneider, Bohdan; Gelly, Jean-Christophe; de Brevern, Alexandre G.; Cerny, Jiri
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Automatic workflow for the classification of local DNA conformations

Bmc Bioinformatics
2013 | Journal article
DOI: 10.1186/1471-2105-14-205
WOSUID:

WOS:000321006500001
Contributors: Cech, P.; Kukal, J.; Cerny, J.; Schneider, B.; Svozil, D.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: Complex theoretical and experimental studies

Biophysical Chemistry
2013 | Journal article
DOI: 10.1016/j.bpc.2013.07.009
WOSUID:

WOS:000324898700015
Contributors: Kratochvilova, I.; Vala, M.; Weiter, M.; Sperova, M.; Schneider, B.; Pav, O.; Sebera, J.; Rosenberg, I.; Sychrovsky, V.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Design and Testing of High-Affinity Mutants of Interferon Gamma Receptor 1

Biophysical Journal
2013 | Journal article
DOI: 10.1016/j.bpj.2012.11.3091
WOSUID:

WOS:000316074305346
Contributors: Mikulecky, P.; Cerny, J.; Biedermannova, L.; Sebo, P.; Schneider, B.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Evolution of REP diversity: a comparative study

Bmc Genomics
2013 | Journal article
DOI: 10.1186/1471-2164-14-385
WOSUID:

WOS:000320611300001
Contributors: Nunvar, J.; Licha, I.; Schneider, B.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Increasing Affinity of Interferon-gamma Receptor 1 to Interferon-gamma by Computer-Aided Design

Biomed Research International
2013 | Journal article
DOI: 10.1155/2013/752514
WOSUID:

WOS:000325638500001
Contributors: Mikulecky, P.; Cerny, J.; Biedermannova, L.; Petrokova, H.; Kuchar, M.; Vondrasek, J.; Maly, P.; Sebo, P.; Schneider, B.
Source: Self-asserted source
Bohdan Schneider via ResearcherID
grade
Preferred source (of 2)‎

Bioinformatic Analysis of the Protein/DNA Interface

Biophysical Journal
2011 | Journal article
WOSUID:

WOS:000306288600363
Contributors: Schneider, B.; Cerny, J.; Svozil, D.; Joseph, A. P.; Gelly, J. C.; de Brevern, A. G.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Bioinformatic Analysis of the Protein/DNA Interface

Biophysical Journal
2011 | Journal article
Contributors: Schneider, B.; Cerny, J.; Svozil, D.; Joseph, A. P.; Gelly, J. C.; de Brevern, A. G.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Calculating the Response of NMR Shielding Tensor sigma(P-31) and (2)J(P-31,C-13) Coupling Constants in Nucleic Acid Phosphate to Coordination of the Mg2+ Cation

Journal of Physical Chemistry A
2011 | Journal article
DOI: 10.1021/jp1114114
WOSUID:

WOS:000288400900037
Contributors: Benda, L.; Schneider, B.; Sychrovsky, V.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

A short survey on protein blocks

Biophys. Rev.
2010 | Journal article
DOI: 10.1007/s12551-010-0036-1
Contributors: Joseph, Agnel Praveen; Agarwal, Garima; Mahajan, Swapnil; Gelly, Jean-Christophe; Swapna, Lakshmipuram S.; Offmann, Bernard; Cadet, Frédéric; Bornot, Aurélie; Tyagi, Manoj; Valadié, Hélène et al.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Charge Transport in DNA Oligonucleotides with Various Base-Pairing Patterns

Journal of Physical Chemistry B
2010 | Journal article
DOI: 10.1021/jp100264v
WOSUID:

WOS:000276563000027
Contributors: Kratochvilova, I.; Todorciuc, T.; Kral, K.; Nemec, H.; Buncek, M.; Sebera, J.; Zalis, S.; Vokacova, Z.; Sychrovsky, V.; Bednarova, L. et al.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Structure and Dynamics of the ApA, ApC, CpA, and CpC RNA Dinucleoside Monophosphates Resolved with NMR Scalar Spin-Spin Couplings

Journal of Physical Chemistry B
2009 | Journal article
DOI: 10.1021/jp809762b
WOSUID:

WOS:000262665500042
Contributors: Vokacova, Z.; Budesinsky, M.; Rosenberg, I.; Schneider, B.; Sponer, J.; Sychrovsky, V.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Building of RNA and DNA double helices into electron density

Acta Crystallographica Section D-Biological Crystallography
2008 | Journal article
DOI: 10.1107/s0907444908007075
WOSUID:

WOS:000255870800002
Contributors: Pavelcik, F.; Schneider, B.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Conductivity of natural and modified DNA measured by scanning tunneling microscopy. The effect of sequence, charge and stacking

Biophysical Chemistry
2008 | Journal article
DOI: 10.1016/j.bpc.2008.08.005
WOSUID:

WOS:000260662900002
Contributors: Kratochvilova, I.; Kral, K.; Buncek, M.; Viskova, A.; Nespurek, S.; Kochalska, A.; Todorciuc, T.; Weiter, M.; Schneider, B.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Effect of local sugar and base geometry on (13)C and (15)N magnetic shielding anisotropy in DNA nucleosides

Journal of Biomolecular Nmr
2008 | Journal article
DOI: 10.1007/s10858-008-9278-7
WOSUID:

WOS:000260281800006
Contributors: Brumovska, E.; Sychrovsky, V.; Vokacova, Z.; Sponer, J.; Schneider, B.; Trantirek, L.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

Rna-a Publication of the Rna Society
2008 | Journal article
DOI: 10.1261/rna.657708|ISSN 1355-8382
WOSUID:

WOS:000253565400010
Contributors: Richardson, J. S.; Schneider, B.; Murray, L. W.; Kapral, G. J.; Immormino, R. M.; Headd, J. J.; Richardson, D. C.; Ham, D.; Hershkovits, E.; Williams, L. D. et al.
Source: Self-asserted source
Bohdan Schneider via ResearcherID

Scanning tunneling spectrosopy study of DNA conductivity

Central European Journal of Physics
2008 | Journal article
DOI: 10.2478/s11534-008-0072-7
WOSUID:

WOS:000257770700005
Contributors: Kratochvilova, I.; Kral, K.; Buncek, M.; Nespurek, S.; Todorciuc, T.; Weiter, M.; Navratil, J.; Schneider, B.; Pavluch, J.
Source: Self-asserted source
Bohdan Schneider via ResearcherID
Items per page:
Page 1 of 3

Peer review (3 reviews for 2 publications/grants)

Review activity for PLoS biology. (1)
Review activity for Structure. (2)
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