Modeling of Biomolecules
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
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 – MC250P03B Biochemistry II
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