Laboratory of Biomolecular Recognition

Detailed laboratory website: https://biorecognition.structbio.org/index.html

Our goal is to understand how biological functions relate to structures of biomolecules and their interactions. We therefore concentrate on determination of biomolecular structures and dynamics of their behavior and study specific protein-protein and protein-DNA interactions, their mutual recognition. In our work, we take advantage of experimental and computational methods of protein engineering, structural biology, bionformatics, and molecular modeling.

In the lab, we run several projects:

• Cytokines. We study structure-function relationships of cytokines from the family of Interleukin 10. These signaling proteins and their receptors are important in the immunity response to viral and bacterial infection, and errors in their regulation cause serious autoimmune and/or allergic health disorders and may even promote malignancy. We concentrate on structural aspects of the cytokine interactions, determine their crystal structures, and modify their molecules to make them more stable. We also apply methods of directed evolution (ribosome and yeast display) to develop de novo proteins binding specifically FIL-10 cytokines or their receptors.
• Bioinformatics. The lab concentrates on structural analysis of nucleic acids, DNA and RNA, and on hydration around proteins and nucleic acids.

Nucleic acids are structurally plastic molecules. To identify their structural polymorphisms we analyzed structures of dinucleotide building blocks in thousands of crystal structures. We clustered them into so called conformational classes NtC and so called structural alphabet CANA. The work is summarized in several publications and the results are available on the website dnatco.org.

Hydration. Water molecules in the first hydration shell of amino acids residues in proteins and dinucleotides in DNA are well ordered and the structure of the shell depends on the biomolecular structure and its sequence.

• Single stranded DNA (ssDNA). ssDNA is known to play important yet largely unknown functions in genome regulation. We study one specific class of bacterial ssDNA, so called Repetitive extragenic palindromes (REP) and their associated enzyme, tyrosine transposase (RAYT).
• Dynamics of Biomolecules. In collaboration with colleagues at ELI-Beamlines, we explore new frontiers in light and optics to create breakthrough science about biomolecular dynamics from femtoseconds to seconds.

Collaborations. The lab is a part of the Institute of Biotechnology of the Czech Academy of Sciences located at the BIOCEV center. It participates in the research program "Structural Biology and Protein Engineering”. We are also active in Instruct-ERIC and ELIXIR (3D-Bioinfo community) infrastructural projects.

2024

• Andrikopoulos PC, Čabart P. "The chromatin remodeler SMARCA5 binds to d-block metal supports: Characterization of affinities by IMAC chromatography and QM analysis." PLoS One. 2024 Oct 7;19(10):e0309134. https://doi.org/10.1371/journal.pone.0309134, PMID: 39374200; PMCID: PMC11458017.

• Herynek Š, Svoboda J, Huličiak M, Peleg Y, Škultétyová Ľ, Mikulecký P, Schneider B. Increasing recombinant protein production in E. coli via FACS-based selection of N-terminal coding DNA libraries. FEBS J. 2024 Dec 26. https://doi.org/10.1111/febs.17376, Epub ahead of print. PMID: 39726159.

• Krattenmacher J, Lera-Ramirez M, Beber A, Herynek S, Grycova L, Liu X, Neuzil P, Nedelec F, Diez S, Braun M, Lansky Z. "Ase1 selectively increases the lifetime of antiparallel microtubule overlaps." Curr Biol. 2024 Sep 9;34(17):4071-4080.e6. https://doi.org/10.1016/j.cub.2024.07.055, Epub 2024 Aug 12. PMID: 39137787.

• Leonard EK, Tomala J, Gould JR, Leff MI, Lin JX, Li P, Porter MJ, Johansen ER, Thompson L, Cao SD, Hou S, Henclova T, Huliciak M, Sargunas PR, Fabilane CS, Vaněk O, Kovar M, Schneider B, Raimondi G, Leonard WJ, Spangler JB. "Engineered cytokine/antibody fusion proteins improve IL-2 delivery to pro-inflammatory cells and promote antitumor activity." JCI Insight. 2024 Sep 24;9(18):e173469. https://doi.org/10.1172/jci.insight.173469, PMID: 39115939; PMCID: PMC11457862.

• Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Černý J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant MG, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nat Methods. 2024 Jul;21(7):1340-1348. https://doi.org/10.1038/s41592-024-02321-7, Epub 2024 Jun 25. PMID: 38918604; PMCID: PMC11526832.

2023

• Huliciak, M., Biedermanova, L., Berdar, D., Herynek, S., Kolarova, L., Tomala, J., Mikulecky, P., & Schneider, B. (2023)."Combined in vitro and cell-based selection display method producing specific binders against IL-9 receptor in high yields."FEBS J. https://doi.org/10.1111/febs.16726

• Chaudhari, A. S., Chatterjee, A., Domingos, C. A. O., Andrikopoulos, P. C., Liu, Y., Andersson, I., Schneider, B., Lorenz-Fonfria, V. A., & Fuertes, G. (2023)."Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222." Protein Sci, e4590. https://doi.org/10.1002/pro.4590

• Kolenko P, Mikulecký P, Pham PN, Malý M, Schneider B. Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10. J Appl Crystallogr. 2023 Jun 16;56(Pt 4):1261-1266. https://doi.org/10.1107/S160057672300479X, PMID: 37555209; PMCID: PMC10405593.

• Liu, Y., Chaudhari, A. S., Chatterjee, A., Andrikopoulos, P. C., Picchiotti, A., Rebarz, M., Kloz, M., Lorenz-Fonfria, V. A., Schneider, B., & Fuertes, G. (2023)."Sub-Millisecond Photoinduced Dynamics of Free and EL222-Bound FMN by Stimulated Raman and Visible Absorption Spectroscopies."Biomolecules, 13(1). https://doi.org/10.3390/biom13010161

• Osickova A, Knoblochova S, Bumba L, Man P, Kalaninova Z, Lepesheva A, Jurnecka D, Cizkova M, Biedermannova L, Goldsmith JA, Maynard JA, McLellan JS, Osicka R, Sebo P, Masin J. "A conserved tryptophan in the acylated segment of RTX toxins controls their β2 integrin-independent cell penetration." J Biol Chem. 2023 Aug;299(8):104978. https://doi.org/10.1016/j.jbc.2023.104978, Epub 2023 Jun 28. PMID: 37390987; PMCID: PMC10392135.

• Pham PN, Zahradník J, Kolářová L, Schneider B, Fuertes G. "Regulation of IL-24/IL-20R2 complex formation using photocaged tyrosines and UV light." Front Mol Biosci. 2023 Jul 7;10:1214235. https://doi.org/10.3389/fmolb.2023.1214235, PMID: 37484532; PMCID: PMC10361524.

• Picchiotti A, Precek M, Zymaková A, Erichlandwehr T, Liu Y, Wiste T, Kahan P, Fernandez-Cuesta I, Andreasson J. "Engraving of stainless-steel wires to improve optical quality of closed-loop wire-guided flow jet systems for optical and X-ray spectroscopy." Front Mol Biosci. 2023 Jun 14;10:1079029. https://doi.org/10.3389/fmolb.2023.1079029, PMID: 37388247; PMCID: PMC10300417.

• Schneider B, Sweeney BA, Bateman A, Cerny J, Zok T, Szachniuk M. "When will RNA get its AlphaFold moment?" Nucleic Acids Res. 2023 Oct 13;51(18):9522-9532. https://doi.org/10.1093/nar/gkad726, PMID: 37702120; PMCID: PMC10570031.

• Svoboda J, Berdár D, Kolenko P, Černý J, Nováková Z, Pavlíček J, Schneider B. "Conformation-based refinement of 18-mer DNA structures." Acta Crystallogr D Struct Biol. 2023 Jul 1;79(Pt 7):655-665. https://doi.org/10.1107/S2059798323004679, Epub 2023 Jun 20. PMID: 37338420; PMCID: PMC10306069.

2022

• Berman, H. M., Lawson, C. L., Schneider, B. (2022). "Developing Community Resources for Nucleic Acid Structures." Life (Basel), 12(4). https://doi.org/10.3390/life12040540

• Biedermannova, L., Cerny, J., Maly, M., Nekardova, M., & Schneider, B. (2022). "Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks." Acta Crystallogr D Struct Biol, 78(Pt 8), 1032-1045. https://doi.org/10.1107/S2059798322006234

• Kipouros, I., Stanczak, A., Ginsbach, J. W., Andrikopoulos, P. C., Rulisek, L., Solomon, E. I."Elucidation of the tyrosinase/O2/monophenol ternary intermediate that dictates the monooxygenation mechanism in melanin biosynthesis." Proc Natl Acad Sci U S A, 119(33), e2205619119. https://doi.org/10.1073/pnas.2205619119

• Klimova N, Holubova J, Streparola G, Tomala J, Brazdilova L, Stanek O, Bumba L, Sebo P. "Pertussis toxin suppresses dendritic cell-mediated delivery of B. pertussis into lung-draining lymph nodes." PLoS Pathog. 2022 Jun 6;18(6):e1010577. https://doi.org/10.1371/journal.ppat.1010577, PMID: 35666769; PMCID: PMC9216613.

• VanDyke D, Iglesias M, Tomala J, Young A, Smith J, Perry JA, Gebara E, Cross AR, Cheung LS, Dykema AG, Orcutt-Jahns BT, Henclová T, Golias J, Balolong J, Tomasovic LM, Funda D, Meyer AS, Pardoll DM, Hester J, Issa F, Hunter CA, Anderson MS, Bluestone JA, Raimondi G, Spangler JB. Engineered human cytokine/antibody fusion proteins expand regulatory T cells and confer autoimmune disease protection. Cell Rep. 2022 Oct 18;41(3):111478. https://doi.org/10.1016/j.celrep.2022.111478, PMID: 36261022; PMCID: PMC9631798.

2021

• Andersson I, Carlsson GH, Hasse D. "Structural Analysis of Strigolactone-Related Gene Products." Methods Mol Biol. 2021;2309:245-257. https://doi.org/10.1007/978-1-0716-1429-7_19, PMID: 34028692.

• Andrikopoulos, P. C., Chaudhari, A. S., Liu, Y., Konold, P. E., Kennis, J. T. M., Schneider, B., & Fuertes, G. "QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors." Phys Chem Chem Phys, 23(25), 13934-13950. https://doi.org/10.1039/d1cp00447f

• Dedecek, J., Tabor, E., Andrikopoulos, P. C., Sklenak, S. "Splitting dioxygen over distant binuclear transition metal cationic sites in zeolites. Effect of the transition metal cation." Int. Journal of Quantum Chemistry, 121(10). https://doi.org/10.1002/qua.26611,  

• Kolarova, L., Zahradnik, J., Huliciak, M., Mikulecky, P., Peleg, Y., Shemesh, M., Schreiber, G., Schneider, B. "De novo developed protein binders mimicking Interferon lambda signaling." FEBS J. https://doi.org/10.1111/febs.16300

• Pham PN, Huličiak M, Biedermannová L, Černý J, Charnavets T, Fuertes G, Herynek Š, Kolářová L, Kolenko P, Pavlíček J, Zahradník J, Mikulecky P, Schneider B. "Protein Binder (ProBi) as a New Class of Structurally Robust Non-Antibody Protein Scaffold for Directed Evolution." Viruses. 2021 Jan 27;13(2):190. https://doi.org/10.3390/v13020190, PMID: 33514045; PMCID: PMC7911045.

• Zahradnik, J., Dey, D., Marciano, S., Kolarova, L., Charendoff, C. I., Subtil, A., Schreiber, G. "A Protein-Engineered, Enhanced Yeast Display Platform for Rapid Evolution of Challenging Targets." ACS Synth Biol. https://doi.org/10.1021/acssynbio.1c00395, Epub 2021 Nov 22. PMID: 34809429; PMCID: PMC8689690.

  2020

• Andrikopoulos PC , Liu Y , Picchiotti A , Lenngren N , Kloz M , Chaudhari AS , Precek M , Rebarz M , Andreasson J , Hajdu J , Schneider B , Fuertes G . "Femtosecond-to-nanosecond dynamics of flavin mononucleotide monitored by stimulated Raman spectroscopy and simulations." Phys Chem Chem Phys. 2020 Mar 28;22(12):6538-6552. https://doi.org/10.1039/c9cp04918e, Epub 2020 Jan 29. PMID: 31994556.

• Černý J, Božíková P, Malý M, Tykač M, Biedermannová L, Schneider B. "Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org." Acta Crystallogr D Struct Biol. 2020 Sep 1;76(Pt 9):805-813. https://doi.org/10.1107/S2059798320009389, Epub 2020 Aug 17. PMID: 32876056; PMCID: PMC7466747.

• Černý J, Božíková P, Svoboda J, Schneider B. "A unified dinucleotide alphabet describing both RNA and DNA structures." Nucleic Acids Res. 2020 Jun 19;48(11):6367-6381. https://doi.org/10.1093/nar/gkaa383, PMID: 32406923; PMCID: PMC7293047.

• Kolenko P, Svoboda J, Černý J, Charnavets T, Schneider B. "Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches." Acta Crystallogr D Struct Biol. 2020 Dec 1;76(Pt 12):1233-1243. https://doi.org/10.1107/S2059798320014151, Epub 2020 Nov 24. PMID: 33263329; PMCID: PMC7709200.

• Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, Soares C, Sussman JL, Thornton JM, Tuffery P, Tusnady G, Wierenga R, Salminen T, Schneider B. "A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)." F1000Res. 2020 Apr 22;9:ELIXIR-278. https://doi.org/10.12688/f1000research.20559.1, PMID: 32566135; PMCID: PMC7284151.

• Pižl M, Picchiotti A, Rebarz M, Lenngren N, Yingliang L, Záliš S, Kloz M, Vlček A. "Time-Resolved Femtosecond Stimulated Raman Spectra and DFT Anharmonic Vibrational Analysis of an Electronically Excited Rhenium Photosensitizer." J Phys Chem A. 2020 Feb 20;124(7):1253-1265. https://doi.org/10.1021/acs.jpca.9b10840, Epub 2020 Feb 5. PMID: 31971382.

• Polovinkin V, Khakurel K, Babiak M, Angelov B, Schneider B, Dohnalek J, Andreasson J, Hajdu J. "Demonstration of electron diffraction from membrane protein crystals grown in a lipidic mesophase after lamella preparation by focused ion beam milling at cryogenic temperatures." J Appl Crystallogr. 2020 Oct 13;53(Pt 6):1416-1424. https://doi.org/10.1107/S1600576720013096, PMID: 33304220; PMCID: PMC7710488.

2019

• Fuertes, G., Nevola, L., Esteban-Martín, S. "Chapter - 9 - Perspectives on drug discovery strategies based on IDPs." Intrinsically Disordered Proteins: 275-327.https://doi.org/10.1016/B978-0-12-816348-1.00009-0

• Zahradník J, Kolářová L, Peleg Y, Kolenko P, Svidenská S, Charnavets T, Unger T, Sussman JL, Schneider B. "Flexible regions govern promiscuous binding of IL-24 to receptors IL-20R1 and IL-22R1." FEBS J. 2019 Oct;286(19):3858-3873. https://doi.org/10.1111/febs.14945, Epub 2019 Jun 12. PMID: 31152679.

2018

• Fuertes G, Banterle N, Ruff KM, Chowdhury A, Pappu RV, Svergun DI, Lemke EA. "Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water". Science. 2018 Aug 31;361(6405):eaau8230. https://doi.org/10.1126/science.aau8230, PMID: 30166461; PMCID: PMC7611747. 

• Palyzová A, Zahradník J, Marešová H, Sokolová L, Kyslíková E, Grulich M, Štěpánek V, Řezanka T, Kyslík P. "Potential of the strain Raoultella sp. KDF8 for removal of analgesics." Folia Microbiol (Praha). 2018 May;63(3):273-282. https://doi.org/10.1007/s12223-017-0563-2, Epub 2017 Nov 11. PMID: 29127620.

• Schneider B, Boǽíková P, Nečasová I, Čech P, Svozil D, Černý J. "A DNA structural alphabet provides new insight into DNA flexibility." Acta Crystallogr D Struct Biol. 2018 Jan 1;74(Pt 1):52-64. https://doi.org/10.1107/S2059798318000050, Epub 2018 Jan 1. PMID: 29372899; PMCID: PMC5786007.

• Zahradník J, Kolářová L, Pařízková H, Kolenko P, Schneider B. "Interferons type II and their receptors R1 and R2 in fish species: Evolution, structure, and function." Fish Shellfish Immunol. 2018 Aug;79:140-152. https://doi.org/10.1016/j.fsi.2018.05.008, Epub 2018 May 6. PMID: 29742458.

• Zahradník J, Kolenko P, Palyzová A, Černý J, Kolářová L, Kyslíková E, Marešová H, Grulich M, Nunvar J, Šulc M, Kyslík P, Schneider B. "The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form." PLoS One. 2018 Apr 9;13(4):e0195299. https://doi.org/10.1371/journal.pone.0195299, PMID: 29630677; PMCID: PMC5891007.

• Zahradník J, Nunvar J, Pařízková H, Kolářová L, Palyzová A, Marešová H, Grulich M, Kyslíková E, Kyslík P. "Agrobacterium bohemicum sp. nov. isolated from poppy seed wastes in central Bohemia." Syst Appl Microbiol. 2018 May;41(3):184-190. https://doi.org/10.1016/j.syapm.2018.01.003, Epub 2018 Jan 31. PMID: 29402492.

2017

• Cerny, J., B. Schneider and L. Biedermannova (2017). "WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations." Phys Chem Chem Phys 19(26): 17094-17102. https://doi.org/10.1039/c7cp00187h

• Křížová L, Kuchař M, Petroková H, Osička R, Hlavničková M, Pelák O, Černý J, Kalina T, Malý P. p19-targeted ABD-derived protein variants inhibit IL-23 binding and exert suppressive control over IL-23-stimulated expansion of primary human IL-17+ T-cells. Autoimmunity. 2017 Mar;50(2):102-113. https://doi.org/10.1080/08916934.2016.1272598, Epub 2017 Jan 19. PMID: 28100093.

• Rohlenova K, Sachaphibulkij K, Stursa J, Bezawork-Geleta A, Blecha J, Endaya B, Werner L, Cerny J, Zobalova R, Goodwin J, Spacek T, Alizadeh Pesdar E, Yan B, Nguyen MN, Vondrusova M, Sobol M, Jezek P, Hozak P, Truksa J, Rohlena J, Dong LF, Neuzil J. Selective Disruption of Respiratory Supercomplexes as a New Strategy to Suppress Her2high Breast Cancer. Antioxid Redox Signal. 2017 Jan 10;26(2):84-103. https://doi.org/10.1089/ars.2016.6677, Epub 2016 Aug 22. PMID: 27392540; PMCID: PMC5206771.

• Schneider, B., P. Bozikova, P. Cech, D. Svozil and J. Cerny (2017). "A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle." Genes (Basel) 8(10). https://doi.org/10.3390/genes8100278, PMID: 29057824; PMCID: PMC5664128.

• Vališ K, Grobárová V, Hernychová L, Bugáňová M, Kavan D, Kalous M, Černý J, Stodůlková E, Kuzma M, Flieger M, Černý J, Novák P. Reprogramming of leukemic cell metabolism through the naphthoquinonic compound Quambalarine B. Oncotarget. 2017 Oct 7;8(61):103137-103153. https://doi.org/10.18632/oncotarget.21663, PMID: 29262552; PMCID: PMC5732718.

2016

• Biedermannová L, Schneider B. "Hydration of proteins and nucleic acids: Advances in experiment and theory." A review. Biochim Biophys Acta. 2016 Sep;1860(9):1821-35. https://doi.org/10.1016/j.bbagen.2016.05.036, Epub 2016 May 27. PMID: 27241846.

• Boukalova S, Stursa J, Werner L, Ezrova Z, Cerny J, Bezawork-Geleta A, Pecinova A, Dong L, Drahota Z, Neuzil J. "Mitochondrial Targeting of Metformin Enhances Its Activity against Pancreatic Cancer." Mol Cancer Ther. 2016 Dec;15(12):2875-2886. https://doi.org/10.1158/1535-7163, MCT-15-1021. Epub 2016 Oct 7. PMID: 27765848.

• Černý J, Božíková P, Schneider B. "DNATCO: assignment of DNA conformers at dnatco.org." Nucleic Acids Res. 2016 Jul 8;44(W1):W284-7. https://doi.org/10.1093/nar/gkw381, Epub 2016 May 5. PMID: 27150812; PMCID: PMC4987927.

• Mikulecký P, Zahradník J, Kolenko P, Černý J, Charnavets T, Kolářová L, Nečasová I, Pham PN, Schneider B. "Crystal structure of human interferon-γ receptor 2 reveals the structural basis for receptor specificity."Acta Crystallogr D Struct Biol. 2016 Sep;72(Pt 9):1017-25. https://doi.org/10.1107/S2059798316012237, Epub 2016 Aug 18. PMID: 27599734; PMCID: PMC5013595.

• Novakova Z, Cerny J, Choy CJ, Nedrow JR, Choi JK, Lubkowski J, Berkman CE, Barinka C. "Design of composite inhibitors targeting glutamate carboxypeptidase II: the importance of effector functionalities." FEBS J. 2016 Jan;283(1):130-43. https://doi.org/10.1111/febs.13557, Epub 2015 Nov 5. PMID: 26460595; PMCID: PMC4712110.

• Taherkhani, M, Armentano, A, Černý, J, Muller-Dethlefs, K. "Threshold ionization spectroscopic investigation of supersonic jet-cooled, laser-desorbed Tryptophan", Chem Phys Lett 657, 16 July 2016, Pages 142-147, https://doi.org/10.1016/j.cplett.2016.05.061

2015

• Biedermannová L, Schneider B. "Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures." Acta Crystallogr D Biol Crystallogr. 2015 Nov;71(Pt 11):2192-202. https://doi.org/10.1107/S1399004715015679, Epub 2015 Oct 27. PMID: 26527137; PMCID: PMC4631476.

• Bocková M, Špringer T, Nečasová I, Nunvar J, Schneider B, Homola J. "Monitoring RAYT activity by surface plasmon resonance biosensor." Anal Bioanal Chem. 2015 May;407(14):3985-93. https://doi.org/10.1007/s00216-015-8491-y, Epub 2015 Jan 31. PMID: 25636231.

• Černý J, Biedermannová L, Mikulecký P, Zahradník J, Charnavets T, Šebo P, Schneider B. "Redesigning protein cavities as a strategy for increasing affinity in protein-protein interaction: interferon- γ receptor 1 as a model." Biomed Res Int. 2015;2015:716945, https://doi.org/10.1155/2015/716945, Epub 2015 Apr 28. PMID: 26060819; PMCID: PMC4427845.

• Craveur P, Joseph AP, Esque J, Narwani TJ, Noël F, Shinada N, Goguet M, Leonard S, Poulain P, Bertrand O, Faure G, Rebehmed J, Ghozlane A, Swapna LS, Bhaskara RM, Barnoud J, Téletchéa S, Jallu V, Cerny J, Schneider B, Etchebest C, Srinivasan N, Gelly JC, de Brevern AG. "Protein flexibility in the light of structural alphabets." Front Mol Biosci. 2015 May 27;2:20. https://doi.org/10.3389/fmolb.2015.00020, PMID: 26075209; PMCID: PMC4445325.

• Charnavets T, Nunvar J, Nečasová I, Völker J, Breslauer KJ, Schneider B. "Conformational diversity of single-stranded DNA from bacterial repetitive extragenic palindromes: Implications for the DNA recognition elements of transposases." Biopolymers. 2015 Oct;103(10):585-96. https://doi.org/10.1002/bip.22666, PMID: 25951997; PMCID: PMC4690160.

• Kluckova K, Sticha M, Cerny J, Mracek T, Dong L, Drahota Z, Gottlieb E, Neuzil J, Rohlena J. "Ubiquinone-binding site mutagenesis reveals the role of mitochondrial complex II in cell death initiation." Cell Death Dis. 2015 May 7;6(5):e1749. https://doi.org/10.1038/cddis.2015.110, PMID: 25950479; PMCID: PMC4669690.

• Osicka R, Osickova A, Hasan S, Bumba L, Cerny J, Sebo P. Bordetella adenylate cyclase toxin is a unique ligand of the integrin complement receptor 3. Elife. 2015 Dec 9;4:e10766. https://doi.org/10.7554/eLife.10766, PMID: 26650353; PMCID: PMC4755762.

2014

• Kuchař M, Vaňková L, Petroková H, Cerný J, Osička R, Pelák O, Sípová H, Schneider B, Homola J, Sebo P, Kalina T, Malý P. "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. 2014 Jun;82(6):975-89. https://doi.org/10.1002/prot.24472, Epub 2013 Nov 23. PMID: 24549990; PMCID: PMC4285857.

• Nunvar J, Elhottova D, Chronakova A, Schneider B, Licha I. "Draft Genome Sequence of Stenotrophomonas maltophilia Strain 5BA-I-2, a Soil Isolate and a Member of a Phylogenetically Basal Lineage." Genome Announc. 2014 Mar 6;2(2):e00134-14. https://doi.org/10.1128/genomeA.00134-14, PMID: 24604648; PMCID: PMC3945504.

• Pavlicek J, Ptacek J, Cerny J, Byun Y, Skultetyova L, Pomper MG, Lubkowski J, Barinka C. "Structural characterization of P1'-diversified urea-based inhibitors of glutamate carboxypeptidase II." Bioorg Med Chem Lett. 2014 May 15;24(10):2340-5. https://doi.org/10.1016/j.bmcl.2014.03.066, Epub 2014 Mar 28. PMID: 24731280; PMCID: PMC4077459.

• Schneider B, Cerný J, Svozil D, Cech P, Gelly JC, de Brevern AG. "Bioinformatic analysis of the protein/DNA interface." Nucleic Acids Res. 2014 Mar;42(5):3381-94. https://doi.org/10.1093/nar/gkt1273, Epub 2013 Dec 11. PMID: 24335080; PMCID: PMC3950675

• Schneider B, Gelly JC, de Brevern AG, Černý J. "Local dynamics of proteins and DNA evaluated from crystallographic B factors." Acta Crystallogr D Biol Crystallogr. 2014 Sep;70(Pt 9):2413-9. https://doi.org/10.1107/S1399004714014631, Epub 2014 Aug 29. PMID: 25195754; PMCID: PMC4157449.

• Vymětal J, Bathula SR, Cerný J, Chaloupková R, Zídek L, Sklenář V, Vondrášek J. "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." Protein Eng Des Sel. 2014 Dec;27(12):463-72. https://doi.org/10.1093/protein/gzu046, Epub 2014 Oct 24. PMID: 25344682.

2013

• Čech P, Kukal J, Černý J, Schneider B, Svozil D. "Automatic workflow for the classification of local DNA conformations." BMC Bioinformatics. 2013 Jun 25;14:205. https://doi.org/10.1186/1471-2105-14-205, PMID: 23800225; PMCID: PMC3694522.

• Kratochvílová I, Vala M, Weiter M, Špérová M, Schneider B, Páv O, Šebera J, Rosenberg I, Sychrovský V. "Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: complex theoretical and experimental studies." Biophys Chem. 2013 Oct-Nov;180-181:127-34. https://doi.org/10.1016/j.bpc.2013.07.009, Epub 2013 Jul 31. PMID: 23968861.

• Mikulecký P, Cerný J, Biedermannová L, Petroková H, Kuchař M, Vondrášek J, Malý P, Šebo P, Schneider B. "Increasing affinity of interferon-γ receptor 1 to interferon-γ by computer-aided design." Biomed Res Int. 2013;2013:752514. https://doi.org/10.1155/2013/752514, Epub 2013 Oct 2. PMID: 24199198; PMCID: PMC3807708.

• Nunvar J, Licha I, Schneider B. "Evolution of REP diversity: a comparative study." BMC Genomics. 2013 Jun 10;14:385. https://doi.org/10.1186/1471-2164-14-385, PMID: 23758774; PMCID: PMC3686654.

2012

• Ahmad JN, Li J, Biedermannová L, Kuchař M, Sípová H, Semerádtová A, Cerný J, Petroková H, Mikulecký P, Polínek J, Staněk O, Vondrášek J, Homola J, Malý J, Osička R, Sebo P, Malý P. "Novel high-affinity binders of human interferon gamma derived from albumin-binding domain of protein G". Proteins. 2012 Mar;80(3):774-89. https://doi.org/10.1002/prot.23234 , Epub 2011 Nov 24. PMID: 22113774.

2011

• Armentano A, Cerný J, Riese M, Taherkhani M, Ben Yezzar M, Müller-Dethlefs K. "Spectral shifts and structures of phenol...Ar(n) clusters." Phys Chem Chem Phys. 2011 Apr 7;13(13):6077-84, https://doi.org/10.1039/c0cp01370f, Epub 2011 Feb 24. PMID: 21347477

• Benda L, Schneider B, Sychrovský V. "Calculating the response of NMR shielding tensor σ(31P) and 2J(31P,13C) coupling constants in nucleic acid phosphate to coordination of the Mg2+ cation." J Phys Chem A. 2011 Mar 24;115(11):2385-95. https://doi.org/10.1021/jp1114114 Epub 2011 Mar 2. PMID: 21366222.

2010

• Joseph AP, Agarwal G, Mahajan S, Gelly JC, Swapna LS, Offmann B, Cadet F, Bornot A, Tyagi M, Valadié H, Schneider B, Etchebest C, Srinivasan N, De Brevern AG. "A short survey on protein blocks." Biophys Rev. 2010 Aug;2(3):137-147. https://doi.org/10.1007/s12551-010-0036-1, Epub 2010 Aug 5. PMID: 21731588; PMCID: PMC3124139.

• Kratochvílová I, Todorciuc T, Král K, Nemec H, Buncek M, Sebera J, Zális S, Vokácová Z, Sychrovský V, Bednárová L, Mojzes P, Schneider B. "Charge transport in DNA oligonucleotides with various base-pairing patterns." J Phys Chem B. 2010 Apr 22;114(15):5196-205. https://doi.org/10.1021/jp100264v, PMID: 20353252.

2009

• Vokácová Z, Budĕsínský M, Rosenberg I, Schneider B, Sponer J, Sychrovský V. "Structure and dynamics of the ApA, ApC, CpA, and CpC RNA dinucleoside monophosphates resolved with NMR scalar spin-spin couplings." J Phys Chem B. 2009 Jan 29;113(4):1182-91. https://doi.org/10.1021/jp809762b, PMID: 19128019.

CESNET Development Fund: 2024 – 0170, B. Schneider: Repository for "Life Sciences" Research Data. 2024

GAČR: GA24-11819S, G. F. Vives: Time-resolved vibrational spectroscopy of proteins assisted by genetically encoded non-canonical amino acids. 2024 – 2026

MŠMT: LX22NPO5102, B. Schneider: National institute for cancer research. 2022 – 2025

MŠMT: EF16_013/0001776, B. Schneider: Czech Infrastructure for Integrative Structural Biology for Human Health. 2017 – 2021

MŠMT: EF15_003/0000447, B. Schneider: Structural dynamics of biomolecular systems. 2016 – 2023

MEYS: LTAUSA18197, Schneider: Design, development, and testing of bioinformatic tools for validation of experimental and computer molecular models in structural biology, biotechnology and pharmacy. 2019-2022.

GACR: GA19-17398S, Schneider: De novo development of bivalent protein binders mimicking the function of interferons lambda. 2019-2021.

MEYS: LM2015047, Schneider: ELIXIR CZ: Czech national infrastructure for biological data. 2016-2019.

GACR: GA16-20507S, Schneider: Interleukins of the IL-10 family: specificity and targeted modulation of interactions with receptors. 2016-2018.

MEYS: CZ.1.07/2.3.00/30.0020, Schneider, Charnavets, Pavlínková, Dodd, Hejnalová: Biotechnological expert. 2012-2015.

GACR: GAP305/12/1801, Schneider: Molecular mechanisms of association of a novel type of transposase with repetitive palindromic elements. 2012-2014.

GACR: GPP205/12/P729, Biedermannová: Effect of protein hydration shell on the stability of protein complexes. 2012-2014.

GACR: GAP305/10/2184, Schneider: Structure-function relationships underlying protein-protein interactions. 2010-2014.

GACR: GAP302/10/0427, Vondrášek: Production and characterization of biologically active recombinant human ameloblastina hard tissue regeneration and differentiation inducing protein. 2010-2012.

MEYS: MEB021032, Schneider: Complex structural analysis of interaction at the protein – nucleic acid interface by unique bioinformatic descriptors. 2010-2011.

Philosophiae Doctor, PhD

Magister of Science, Mgr and Bachelor, Bc

Postdoctoral Fellows