Strukturní bioinformatika proteinů

Strukturní bioinformatika proteinů

Ing. Jiří Černý

Ing. Jiří Černý — Vedoucí projektu

O nás

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

Akce

Publikace

2018

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

2016

Cerny, Jiri; Bozikova, Paulina; Schneider, Bohdan; DNATCO: assignment of DNA conformers at dnatco.org; 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

2015

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

Tým

Ing. Jiří Černý

Ing.
Jiří Černý

Vedoucí skupiny Strukturní bioinformatika proteinů

jiri.cerny@ibt.cas.cz
+420325873738