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Modeling of Biomolecules

Contact; People; Research; Publications; Collaboration; Teaching

 

Contact

Department of Biochemistry, Faculty of Science, Charles University

Hlavova 2030/8, 2. floor, room 215

tel: +420 221 951 280

e-mail: vaclav.martinek(at)natur.cuni.cz

 

People

Václav Martínek

Petr Jeřábek

Jaroslav Stránský - Bc. student

 

Research

Metabolizmus cizorodých látek Metabolism of Xenobiotic Compounds

- cytochrome P450s, cytochrome b5 and other reticular proteins

Development of a Lyme Disease vaccine

- construction of thermostable fragments of OspA proteins

Signalling proteins of human pathogenes

- kinases, phosphatases and signalling  nucleotides

 

Methods

Molecular dynamics

- simulation of protein dynamics in real time at atomic level

Protein-protein docking

- predikce struktur proteinových komplexů

Protein-ligand docking

- prediction of protein-ligand complexes

Homology modeling

- prediction of a protein structure based on its relative proteins

 

Publications

Kuipers K., Gallay C., Martínek V., Rohde M., Martínková M., van der Beek S.L., Jong W.S., Venselaar H., Zomer A., Bootsma H., Veening J.W., de Jonge M.I. 2016 Highly conserved nucleotide phosphatase essential for membrane lipid homeostasis in Streptococcus pneumoniae 101(1):12-26 IF2016=3.898

Martínek V., Bárta F., Hodek P., Frei E., Schmeiser H.H., Arlt V.M., Stiborová M. 2017: Comparison of the oxidation of carcinogenic aristolochic acid I and II by microsomal cytochromes P450 in vitro: experimental and theoretical approaches. Monatshefte für Chemie 148(11):1971-1981 IF2017=1.285

Jeřábek P., Florián J, and Martínek V. 2016: Membrane-anchored cytochrome P450 1A2–cytochrome b5 complex: Structure and dynamics. Chemical Research in Toxicology 29: 626-636 IF2016= 4.123

Jeřábek P., Florián J, and Martínek V. 2016: Lipid molecules can induce an opening of membrane-facing tunnels in cytochrome P450 1A2. Physical Chemistry Chemical Physics 14:30344-30356 IF2016= 3.278

Jeřábek P., Florián J, Stiborova M. and Martínek V. 2014: Flexible Docking-Based Molecular Dynamics/Steered Molecular Dynamics Calculations of Protein–Protein Contacts in a Complex of Cytochrome P450 1A2 with Cytochrome b5. Biochemistry 53: 6695-6705 IF2014=3.015

 

Collaboration

Jan Florián, Loyola University Chicago, Spojené státy americké

Milan Raška, Univerzita Paleckého v Olomouci, Česká republika

Marien I. de Jonge, Radboud University Medical Center, Nizozemsko

 

Teaching (Department of Biochemistry, PřF UK)

MC250P07B Internet and Bioinformatics

MC250C17N Advanced practical course in Biochemistry I

MC250C03    Advanced practical course in Biochemistry I for KATA

MC250P03B Biochemistry II

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