Structural Bioinformatics of Proteins

Structural Bioinformatics of Proteins

Ing. Jiří Černý

Ing. Jiří Černý — Project head

The Institute of Biotechnology of the Czech Academy of Sciences

About us

The research concentrates on understanding the structural and functional features of biologically relevant molecules and their interactions employing the tools of Structural Bioinformatics and Molecular Modeling. We closely collaborate with researchers within BIOCEV as well as with external groups on analysis of structural data, rational design of protein mutations, and design of ligands and inhibitors of studied proteins.

The main topics include:

  • Development and testing of computational methods and procedures for modeling of structure and properties of biomolecules and their complexes.
  • Development of novel computational methods and parameter optimization for description of designed ligands and inhibitors and their interactions.
  • Analysis of conformational behavior of oligopeptide blocks in proteins.
  • Design and identification of stable protein folds suitable for mutagenesis.
  • Identification of key protein residues involved in recognition and strength of interaction.


Offered expertise:

  • Homology modeling
  • Molecular dynamics simulations (MD)
  • Ab initio quantum chemical calculations
  • In silico mutagenesis
  • Protein/protein docking
  • Protein/small molecule docking




Cerny, J., Bozikova, P., Balik, A., Marques, S.M., Vyklicky, L. NMDA Receptor Opening and Closing-Transitions of a Molecular Machine Revealed by Molecular Dynamics. Biomolecules, 9(10): 546, 2019. doi: 10.3390/biom9100546. ISSN: 2218-273X.

Frolikova, M., Valaskova, E., Cerny, J., Lumeau, A., Sebkova, N., Palenikova, V., Sanches-Hernandez, N., Pohlova, A., Manaskova-Postlerova, P., Dvorakova-Hortova, K. Addressing the Compartmentalization of Specific Integrin Heterodimers in Mouse Sperm. International Journal of Molecular Sciences, 20(5): 1004, 2019. doi:10.3390/ijms20051004. ISSN: 1422-0067.

Peter E.K., Cerny J. A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints. International Journal of Molecular Sciences, 20(2): 370, 2019. doi: 10.3390/ijms20020370. eISSN: 1422-0067.

Plavec, T.V., Kuchar, M., Benko, A., Liskova, V., Cerny, J., Berlec, A., Maly, P. Engineered Lactococcus lactis Secreting IL-23 Receptor-Targeted REX Protein Blockers for Modulation of IL-23/Th17-Mediated Inflammation. Microorganisms, 7(5): 152, 2019. doi: 10.3390/microorganisms7050152. EISSN 2076-2607.

Kosztyu, P; Kuchar, M; Cerny, J; Barkocziova, L; Maly, M; Petrokova, H; Czernekov, L; Liskova, V; Raskova Kafkova, L; Knotigova, P; Masek, J; Turanek, J; Maly, P; Raska, M; Proteins mimicking epitope of HIV-1 virus neutralizing antibody induce virus-neutralizing sera in mice. EBioMedicine, Sep;47:247-256, 2019. doi:10.1016/j.ebiom.2019.07.015


Frolikova, M., Manaskova-Postlerova, P., Cerny, J., Jankovicova, J., Simonik, O., Pohlova, A., Secova, P., Antalikova, J., Dvorakova-Hortova, K. CD9 and CD81 Interactions and Their Structural Modelling in Sperm Prior to Fertilization. International Journal of Molecular Sciences,19(4): 1236, 2018. doi: 10.3390/ijms19041236. eISSN: 1422-0067.

Hlavničková M., Kuchař M., Osička R., Vaňková L., Petroková H., Malý M., Černý J., Arenberger P., Malý P. ABD-Derived Protein Blockers of Human IL-17 Receptor A as Non-IgG Alternatives for Modulation of IL-17-Dependent Pro-Inflammatory Axis. International Journal of Molecular Sciences, 19(10): 3089, 2018. doi: 10.3390/ijms19103089. eISSN: 1422-0067.

Peter E.K., Cerny J. Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank. International Journal of Molecular Sciences, 19(11), 3405, 2018. doi: 10.3390/ijms19113405. eISSN: 1422-0067.

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.

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, 13(4): e0195299, 2018. doi: 10.1371/journal.pone.0195299. eISSN: 1932-6203.

Schneider, B., Bozikova, P., Necasova, I., Cech, P., Svozil, D., Cerny, J. A DNA structural alphabet provides new insight into DNA flexibility. Acta Crystallographica Section D STRUCTURAL BIOLOGY, 74(1): 52-64, 2018. doi: 10.1107/S2059798318000050. ISSN: 2059-7983.

Skrlec, K., Zadravec, P., Hlavnickova, M., Kuchar, M., Vankova, L., Petrokova, H., Krizova, L., Cerny, J., Berlec, A., Maly, P. p19-Targeting ILP Protein Blockers of IL-23/Th-17 Pro-Inflammatory Axis Displayed on Engineered Bacteria of Food Origin. International Journal of Molecular Sciences, 19(7): 1933, 2018. doi: 10.3390/ijms19071933. ISSN 1422-0067.

Ladislav, Marek; Cern, Jiri; Krusek, Jan; Horak, Martin; Balik, Ales; Vyklicky, Ladislav; The LILI Motif of M3-S2 Linkers Is a Component of the NMDA Receptor Channel Gate. Front. Mol. Neurosci.; 06 April 2018; doi: 10.3389/fnmol.2018.00113.

Vyklicky, Vojtech; Krausova, Barbora; Cerny, Jiri; Ladislav, Marek; Smejkalova, Tereza; Kysilov, Bohdan; Korinek, Miloslav; Danacikova, Sarka; Horak, Martin; Chodounska, Hana; Kudova, Eva; Vyklicky, Ladislav; Surface Expression, Function, and Pharmacology of Disease-Associated Mutations in the Membrane Domain of the Human GluN2B Subunit. Front. Mol. Neurosci.; 06 April 2018; doi: 10.3389/fnmol.2018.00110


Cerny, J. Schneider, B., Biedermannova, L. WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations. Physical Chemistry Chemical Physics, 26(19): 17094-17102, 2017. doi: 10.1039/C7CP00187H. ISSN: 1463-9076.

Krizova L., Kuchar M., Petrokova H., Osicka R., Hlavnickova M., Pelak O., Cerny J., Kalina T., Maly 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, 50: 102-113, 2017. doi: 10.1080/08916934.2016.1272598. ISSN 0891-6934.

Rohlenova, K., Sachaphibulkij, K., Stursa, J., Bezawork-Geleta, A., Blecha, J., Endaya, B., Werner, L., Cerny, J., Zobalova, R., Goodwin, J., Spacek, T., Alisadeh, E., Yan, B., Nguyen, M., Vondrusova, M., Sobol, M., Jezek, P., Hozak, P., Truksa, J., Rohlena, J., Dong, L., Neuzil, J. Selective disruption of respiratory supercomplexes as a new strategy to suppress Her2-high breast cancer. Antioxidants & Redox Signaling, 26(2): 84-103, 2017. doi: 10.1089/ars.2016.6677. ISSN 1557-7716.

Schneider, B., Bozikova, P., Cech, P., Svozil, D., Cerny, J. A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle. Genes, 8(10): 278, 2017. doi: 10.3390/genes8100278. eISSN 2073-4425.

Valis, K., Grobarova, V., Hernychova, L., Buganova, M., Kavan, D., Kalous, M., Cerny, J., Stodulkova, E., Kuzma, M., Flieger, M., Cerny, J., Novak, P. Reprogramming of leukemic cell metabolism through the naphthoquinonic compound Quambalarine B. Oncotarget (Advanced Publications), 21663, 2017. doi: 10.18632/oncotarget.21663. eISSN 1949-2553.


Cerny, Jiri; Bozikova, Paulina; Schneider, Bohdan; DNATCO: assignment of DNA conformers at; NUCLEIC ACIDS RESEARCH; 10.1093/nar/gkw381; 2016; IF = 9.112

Vyklicky, Vojtech; Smejkalova, Tereza; Krausova, Barbora; Balik, Ales; Korinek, Miloslav; Borovska, Jirina; Horak, Martin; Chvojkova, Marketa; Kleteckova, Lenka; Vales, Karel; Cerny, Jiri; Nekardova, Michaela; Chodounska, Hana; Kudova, Eva; Vyklicky, Ladislav; Preferential Inhibition of Tonically over Phasically Activated NMDA Receptors by Pregnane Derivatives; JOURNAL OF NEUROSCIENCE; 10.1523/JNEUROSCI.3181-15.2016; 2016; IF = 6.344

Novakova, Zora; Cerny, Jiri; Choy, Cindy J.; Nedrow, Jessie R.; Choi, Joeseph K.; Lubkowski, Jacek; Berkman, Clifford E.; Barinka, Cyril; Design of composite inhibitors targeting glutamate carboxypeptidase II: the importance of effector functionalities; FEBS JOURNAL; 10.1111/febs.13557; 2016; IF = 4.001

Mikulecký, Pavel; Zahradník, Jirí; Kolenko, Petr; Černý, Jiří; Charnavets, Tatsiana; Kolářová, Lucie; Nečasová, Iva; Pham, Phuong Ngoc; Schneidera, Bohdan; Crystal structure of human interferon-γ receptor 2 reveals the structural basis for receptor specificity. Structural Biology, 72(9):1017-1025, 2016. doi: 10.1107/S2059798316012237

Taherkhani, Mehran; Armentano, Antonio; Cerny, Jiri; Muller-Dethlefs, Klaus; Threshold ionization spectroscopic investigation of supersonic jet-cooled, laser-desorbed Tryptophan. Chemical Physics Letters, 657, 16 July 2016, doi: 10.1016/j.cplett.2016.05.061.


Vyklicky, Vojtech; Krausova, Barbora; Cerny, Jiri; Balik, Ales; Zapotocky, Martin; Novotny, Marian; Lichnerova, Katarina; Smejkalova, Tereza; Kaniakova, Martina; Korinek, Miloslav; Petrovic, Milos; Kacer, Petr; Horak, Martin; Chodounska, Hana; Vyklicky, Ladislav; Block of NMDA receptor channels by endogenous neurosteroids: implications for the agonist induced conformational states of the channel vestibule; SCIENTIFIC REPORTS; 10.1038/srep10935; 2015; IF = 5.578

Cerny, Jiri; Biedermannova, Lada; Mikulecky, Pavel; Zahradnik, Jiri; Charnavets, Tatsiana; Sebo, Peter; Schneider, Bohdan; Redesigning Protein Cavities as a Strategy for Increasing Affinity in Protein-Protein Interaction: Interferon-gamma Receptor 1 as a Model; BIOMED RESEARCH INTERNATIONAL; 10.1155/2015/716945; 2015; IF = 1.579

Osicka, Radim; Osickova, Adriana; Hasan, Shakir; Bumba, Ladislav; Cerny, Jiri; Sebo, Peter; Bordetella adenylate cyclase toxin is a unique ligand of the integrin complement receptor 3.; eLife; 10.7554/eLife.10766; 2015; IF = 9.322

Craveur, P; Joseph, A.P.; Esque, J; Narwani, T.J.; Noël, F; Shinada, N; Goguet, M; Leonard, S; Poulain, P; Bertrand, O; Faure, G; Rebehmed, J; Ghozlane, A; Swapna, L.S.; Bhaskara, R.M.; Barnoud, J; Téletchéa, S; Jallu, V; Cerny, J; Schneider, B; Etchebest, C; Srinivasan, N; Gelly, J.C.; de Brevern, A.G.; Protein flexibility in the light of structural alphabets. Front Mol Biosci. 2015 May 27;2:20. doi: 10.3389/fmolb.2015.00020. eCollection 2015.

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:e1749. doi: 10.1038/cddis.2015.110.


Ing. Jiří Černý Ing. Jiří Černý

Jiří Černý

Head of Group Structural Bioinformatics of Proteins