Jiří Vondrášek

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Sodium-dependent transport into astrocytes is critical for maintaining the extracellular concentrations of glutamate below toxic levels in the central nervous system. In this study, the expression of the glial glutamate transporters GLT-1 and GLAST was studied in primary cultures derived from cortical tissue. In primary astrocytes, GLAST protein levels were(More)
Virtual screening is becoming an important tool for drug discovery. However, the application of virtual screening has been limited by the lack of accurate scoring functions. Here, we present a novel scoring function, MedusaScore, for evaluating protein-ligand binding. MedusaScore is based on models of physical interactions that include van der Waals,(More)
The HIV structural database (HIVSDB) is a comprehensive collection of the structures of HIV protease, both of unliganded enzyme and of its inhibitor complexes. It contains abstracts and crystallographic data such as inhibitor and protein coordinates for 248 data sets, of which only 141 are from the Protein Data Bank (PDB). Efficient annotation, indexing,(More)
In order to determine preferred coordination geometries of six divalent cations (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+), two sources of experimental data were exploited: Protein Data Bank and Cambridge Structural Database. Metal-binding sites of approximately 100 metalloproteins and 3000 smaller transition metal complexes were analyzed and classified. The(More)
A novel technique to annotate, query, and analyze chemical compounds has been developed and is illustrated by using the inhibitor data on HIV protease-inhibitor complexes. In this method, all chemical compounds are annotated in terms of standard chemical structural fragments. These standard fragments are defined by using criteria, such as chemical(More)
Interactions between amino acid side chains play a crucial role both within a folded protein and between the interacting protein molecules. Here we have selected a representative set of 24 of the 400 (20 × 20) possible interacting side chain pairs based on data from Atlas of Protein Side-Chain Interactions. For each pair, we obtained its most favorable(More)
1 ́ ˇ 1 ˇ ́ ˇ 1 PAVEL HOBZA, MARTIN KABELAC, JIRI SPONER, ́ 2 ˇ ́ ́ˇ 3 PETR MEJZLIK, JIRI VONDRASEK J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejskova ́ ˇ 3, 128 23 Prague 8, Czech Republic Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Czech Republic ́ Institute of Organic Chemistry(More)
Molecular dynamics simulations show significant like-charge pairing of guanidinium side chains in aqueous poly-arginine, while this effect is absent in aqueous poly-lysine containing ammonium-terminated side chains. This behavior of the guanidinium group is revealed also by protein database searches, having important biochemical implications. Combination of(More)
Human immunodeficiency virus protease (HIV PR) was only discovered as encoded in the HIV genome in 1985, but soon thereafter, this virus-specific enzyme was identified as a crucial target for designing drugs against acquired human immunodeficiency syndrome (AIDS). With six such drugs approved to date since 1995 by the United States Food and Drug(More)
An analysis of the crystal structure of [BmPBP...bombykol] complex identified nine amino acid residues involved in a variety of intermolecular interactions binding the ligand. Using simple model fragments as the representatives of the residues, the interaction energies of their complexes with bombykol were calculated using high-level ab initio methods. The(More)