doc. Ing. Bohdan Schneider, CSc.

doc. Ing. Bohdan Schneider, CSc.

Head of Structural Biology and Protein Engineering Program, Head of the Intermolecular Recognition of Proteins and Nucleic Acids Group

Bohdan Schneider works at the Institute of Biotechnology CAS, where he focuses on protein engineering and on the study of the structure and dynamics of nucleic acids. Analysis of the structural variability of the backbone of both types of nucleic acids, DNA and RNA, has led to the determination of the local structural families of these molecules. In collaboration with colleagues he uses the knowledge of the structural behavior of nucleic acids to develop new computational methods for interpreting data from crystallographic, NMR and other biophysical measurements. He actively participated in the development of basic structural databases of biomolecules – Protein Databank and Nucleic Acid Database.

Citation report:

  • Number of articles (according to WoS): 57
  • Number of citations (according to WoS): over 3000
  • H-Index: 21
  • Number of patents: 0

 

Bohdan Schneider (1957) contributed to structural biology at areas of bioinformatics, biophysics, and crystallography. He studies structure and dynamics of nucleic acids and their recognition by proteins. His main contribution lies in bioinformatic analysis of structures of DNA [Schneider et al. Nucleic Acids Res. doi: 10.1093/nar/gkt1273] and RNA [Schneider et al. Nucleic Acids Res. 32, 1666 (2004)] and in work on DNA solvation [e.g. Schneider & Berman Biophys. J. 69, 2661 (1995)]. In these studies, he has devised and successfully applied novel powerful non-parametric algorithm of filtration of noisy three-dimensional data that allows their structural interpretation.

 

Important is his participation at infrastructure projects. Bohdan Schneider took part in creation of the Nucleic Acid Database [NDB, Berman et al. Biophys. J. 63, 751 (1992)] and was responsible for NDB operations in years 1998-2000. As a long time collaborator of the Protein Databank [PDB, Berman et al. Acta Cryst. D 58, 889 (2002)] he participated on the development of the web-based deposition system that is used by the PDB [Burkhardt et al. PLOS Comput. Biol. 2, 1186 (2006)]. Active involvement in important infrastructure projects of considerable complexity, PDB and NDB, demonstrate his experience with large international teams.

His thorough knowledge about structural biology is corroborated by co-authorship of ten chapters in books that summarize structural behavior of nucleic acids [Schneider & Berman: Basics of Nucleic Acid Structure, in Computational studies of RNA and DNA, Springer (2006) and Neidle et al.: Fundamentals of DNA and RNA structure, in Structural Bioinformatics, Wiley (2009)], describe infrastructure projects [Schneider et al: NDB, in Structural Bioinformatics, Wiley (2009)], and discuss solvation of DNA.

He has Master degree in physical chemistry, defended Ph.D thesis by work on structure-function relationships of antidepressants in 1989, and in 2010 received title DSc from the Academy of Sciences of the Czech Republic for his work on Nucleic structure and dynamics.

Scientific program ―Structural biology and protein engineering‖ of the center BIOCEV will benefit from Bohdan Schneider’s expertise of bioinformatics, biophysics, and crystallography and his experience with day-to-day administration and supervision of international projects.

Recent publications

2016

Mikulecky, P., Zahradnik, J., Kolenko, P., Cerny, J., Charnavets, T., Kolarova, L., Necasova, I., Pham, P. N., Schneider, B. Crystal structure of human interferon-γ receptor 2 reveals the structural basis for receptor specificity. Acta Crystallographica Section D, 72: 1017-1025, 2016. doi: 10.1107/S2059798316012237. ISSN 2059-7983.
 

2015

Jiri Cerny, Lada Biedermannova, Pavel Mikulecky, Jiri Zahradnik, Tatsiana Charnavets, Peter Sebo & Bohdan Schneider: Redesigning protein cavities as a strategy for increasing affinity in protein-protein interaction. Interferon-Îł receptor 1 as a model. BioMed Research International 2015: 716945 (2015). doi: 10.1155/2015/716945.

Tatsiana Charnavets, Jaroslav Nunvar, Iva Necasova, Jens Voelker, Kenneth J. Breslauer & Bohdan Schneider: Conformational Diversity of Single-stranded DNA from Bacterial Repetitive Extragenic Palindromes: Implications for the DNA Recognition Elements of Transposases. Biopolymers, in press (2015). doi: 10.1002/bip.22666.

Pierrick Craveur, Agnel P. Joseph, Jeremy Esque, Tarun J. Narwani, Floriane Noel, Nicolas Shinada, Matthieu Goguet, Sylvain Leonard, Pierre Poulain, Olivier Bertrand, Guilhem Faure, Joseph Rebehmed, Amine Ghozlane, Lakshmipuram S. Swapna, Ramachandra M. Bhaskara, Jonathan Barnoud, Stephane Teletchea, Vincent Jallu, Jiri Cerny, Bohdan Schneider, Catherine Etchebest, Narayanaswamy Srinivasan, Jean-Christophe Gelly & Alexandre G. de Brevern: Protein flexibility in the light of structural alphabets. Frontiers in Molecular Biosciences 2: (2015). doi: 10.3389/fmolb.2015.00020.

Marketa Bockova, Tomas Springer, Iva Necasova, Jaroslav Nunvar, Bohdan Schneider & Jiri Homola: Monitoring RAYT activity by surface plasmon resonance biosensor. Analytical and Bioanalytical Chemistry, 407: 3985-3993 (2015). doi: 10.1007/s00216-015-8491-y.

Biedermannova, L., Schneider, B. Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures. Acta Crystallographica D (2015) 71:2192-202. doi: 10.1107/S1399004715015679. ISSN 1399-0047.

2014

Milan Kuchar, Lucie Vankova, Hana Petrokova, Jiri Cerny, Radim Osicka, Ondrej Pelak, Hana Sipova, Bohdan Schneider, Jiri Homola, Peter Sebo, Tomas Kalina & Petr Maly: 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 82, 975-989 (2014). doi:10.1002/prot.24472.

Bohdan Schneider, Jiri Cerny, Daniel Svozil, Petr Cech, Jean-Christophe Gelly & Alexandre G. de Brevern: Bioinformatic analysis of the protein/DNA interface. Nucleic Acids Res. 42, 3381-3394 (2014). doi: 10.1093/nar/gkt1273.

Bohdan Schneider, Jean-Christophe Gelly, Alexandre G. de Brevern & Jiri Cerny: Local dynamics of proteins and DNA evaluated from crystallographic B-factors. Acta Crystallographica D 70: 2413 (2014). doi:10.1107/S1399004714014631.

Jaroslav Nunvar, Dana Elhottova, Alena Chronakova, Bohdan Schneider & Irena Licha: Draft Genome Sequence of Stenotrophomonas maltophilia Strain 5BA-I-2, a Soil Isolate and a Member of a Phylogenetically Basal Lineage. Genome Announc. 2: e00134-14 (2014). doi: 10.1128/genomeA.00134-14.

2013

Pavel Mikulecky, Jiri Cerny, Lada Biedermannova, Hana Petrokova, Milan Kuchar, Jiri Vondrasek, Petr Maly, Peter Sebo & Bohdan Schneider: Increasing affinity of interferon-gamma receptor 1 to interferon-gamma by computer-aided design. BioMed Research International 2013, 12 pages, (2013). doi: 10.1155/2013/752514.

Petr Cech, Jaromir Kukal, Jiri Cerny, Bohdan Schneider & Daniel Svozil: Automatic workflow for the classification of local DNA conformations. BMC Bioinformatics, 14, 205 (2013). doi:10.1186/1471-2105-14-205

Jaroslav Nunvar, Irena Licha & Bohdan Schneider: Evolution of REP diversity: a comparative study. BMC Genomics 14:385m (2013). doi:10.1186/1471-2164-14-385.

2010

Agnel Praveen Joseph, Garima Agarwal, Swapnil Mahajan, Jean-Christophe Gelly, Lakshmipuram S. Swapna, Bernard Offmann, Frederic Cadet, Aurelie Bornot, Manoj Tyagi, Helene Valadie, Bohdan Schneider, Catherine Etchebest, Narayanaswamy Srinivasan & Alexandre G. de Brevern: A short survey on protein blocks. Biophys Rev. 2, 137-145 (2010). doi: 10.1007/s12551-010-0036-1.

2008

Daniel Svozil, Jan Kalina, Marek Omelka & Bohdan Schneider: DNA Conformations and Their Sequence Preferences. Nucleic Acids Res. 36, 3690-3704 (2008). doi: 10.1093/nar/gkn260.

Jane S. Richardson, Bohdan Schneider, Laura W. Murray, Gary J. Kapral, Robert M. Immormino, Jeffrey J. Headd, David C. Richardson, Daniela Ham, Eli Hershkovits, Loren Dean Williams, Kevin S. Keating, Anna Marie Pyle, David Micallef, John Westbrook & Helen M. Berman: RNA Backbone: Consensus All-angle Conformers and Modular String Nomenclature. RNA 14: 465-481 (2008). doi: 10.1261/rna.657708.

Frantisek Pavelcik & Bohdan Schneider: Building of RNA and DNA double helices into electron density. Acta Cryst. D64, 620-626 (2008). doi: 10.1107/S0907444908007075

Irena Kratochvilova, Karel Kral, Martin Buncek, Alena Viskova, Stanislav Nespurek, Anna Kochalska, Tatiana Todorciuc, Martin Weiter & Bohdan Schneider: Conductivity of natural and modified DNA measured by scanning tunneling microscopy. The effect of sequence, charge and stacking. Biophys. Chem. 6, 422-426 (2008). doi: 10.1016/j.bpc.2008.08.005

2006

Kyle Burkhardt, Bohdan Schneider & Jeramia Ory: A Biocurator Perspective: Annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank. PLOS Comp.Biol. 2, 1186-1189 (2006).

2005

Wei Ge, Bohdan Schneider & Wilma.K. Olson: Knowledge-Based Elastic Potentials for Docking Drugs or Proteins with Nucleic Acids. Biophys. J. 88, 1166-1190 (2005).

2004

Bohdan Schneider, Zdenek Moravek & Helen M. Berman: RNA Conformational Classes. Nucleic Acids Res. 32, 1666-1677 (2004).

2002

Zdenek Moravek, Stephen Neidle & Bohdan Schneider: Protein and Drug Interactions in the Minor Groove of B-DNA. Nucleic Acids Res. 30, 1182-1191 (2002).

Helen M. Berman, John Westbrook, Zukang Feng, Lisa lype, Bohdan Schneider, Christine Zardecki: The Nucleic Acid Database. Acta Cryst. D58, 889-898 (2002).

Helen M. Berman, Tammy Battistuz, T. N. Bhat, Wolfgang F. Bluhm, Philip E. Bourne, Kyle Burkhardt, Zukang Feng, Gary L Gilliland, Lisa lype, Shri Jain, Phoebe Fagan, Jessica Marvin, David Padilla, Veerasamy Ravichandran, Bohdan Schneider, Narmada Thanki, Helge Weissig, John D. Westbrook and Christine Zardecki: The Protein Data Bank. Acta Cryst. D58, 899-907 (2002).

1998

A. Harper, J. A. Brannigan, M. Buck, L. Hewitt, R. J. Lewis, M. H. Moore & B. Schneider: The Structure of d(TGCGCA)2 and a Comparison to Other DNA Hexamers. Acta Cryst. D54, 1273 - 1284 (1998).

Bohdan Schneider, Ketan Patel & Helen M. Berman: Hydration of the Phosphate Group in Double-Helical DNA. Biophys. J. 75, 2422-2434 (1998).

Julia Woda, Bohdan Schneider, Ketan Patel, K. Mistry & Helen M. Berman: Protein and Drug Interactions in the Minor Groove of B-DNA. Biophys. J. 75, 2170-2177 (1998).

Bohdan Schneider & Martin Kabelac: Stereochemistry of Binding of Metal Cations and Water to a Phosphate Group. J. Am. Chem. Soc. 120, 161-165 (1998).

1996

Bohdan Schneider, Martin Kabelac & Pavel Hobza: Geometry of the Phosphate Group and Its Interactions with Metal Cations in Crystals and ab Initio Calculations. J. Am. Chem. Soc. 118, 12207-12217 (1996).

1995

Bohdan Schneider & Helen M. Berman: Hydration of the DNA Bases Is Local. Biophys. J. 69, 2661-2669 (1995).

1993

Bohdan Schneider, Dawn. M. Cohen, Leo Schleifer, A.R. Srinivasan, Wilma K. Olson & Helen M. Berman: A Systematic Method to Study the Spatial Distribution of Water Molecules around Nucleic Acid Bases. Biophys .J. 65, 2291-2303 (1993).