jiri vondrasek
jiri vondrasek
Institute of Organic Chemistry and Biochemistry, Head of Bioinformatics
Verified email at - Homepage
Cited by
Cited by
Inhibitors of HIV-1 protease: a major success of structure-assisted drug design
A Wlodawer, J Vondrasek
Annual review of biophysics and biomolecular structure 27 (1), 249-284, 1998
Coordination geometries of selected transition metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+) in metalloproteins
L Rulı́šek, J Vondrášek
Journal of inorganic biochemistry 71 (3-4), 115-127, 1998
Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree–Fock method for …
P Hobza, M Kabeláč, J Šponer, P Mejzlík, J Vondrášek
Journal of Computational Chemistry 18 (9), 1136-1150, 1997
Quantification and rationalization of the higher affinity of sodium over potassium to protein surfaces
L Vrbka, J Vondrášek, B Jagoda-Cwiklik, R Vácha, P Jungwirth
Proceedings of the National Academy of Sciences 103 (42), 15440-15444, 2006
MedusaScore: an accurate force field-based scoring function for virtual drug screening
S Yin, L Biedermannova, J Vondrasek, NV Dokholyan
Journal of chemical information and modeling 48 (8), 1656-1662, 2008
Unexpectedly strong energy stabilization inside the hydrophobic core of small protein rubredoxin mediated by aromatic residues: correlated ab initio quantum chemical calculations
J Vondrášek, L Bendová, V Klusák, P Hobza
Journal of the American Chemical Society 127 (8), 2615-2619, 2005
Structure and IR Spectrum of Phenylalanyl–Glycyl–Glycine Tripetide in the Gas‐Phase: IR/UV Experiments, Ab Initio Quantum Chemical Calculations, and Molecular Dynamic Simulations
D Řeha, H Valdes, J Vondrášek, P Hobza, A Abu‐Riziq, B Crews, ...
Chemistry–A European Journal 11 (23), 6803-6817, 2005
The molecular origin of like-charge arginine− arginine pairing in water
J Vondrášek, PE Mason, J Heyda, KD Collins, P Jungwirth
The journal of physical chemistry B 113 (27), 9041-9045, 2009
Quantum chemical benchmark energy and geometry database for molecular clusters and complex molecular systems (www. begdb. com): a users manual and examples
J Řezáč, P Jurečka, KE Riley, J Černý, H Valdes, K Pluháčková, K Berka, ...
Collection of Czechoslovak Chemical Communications 73 (10), 1261-1270, 2008
Structure and stability of the water− graphite complexes
M Rubes, P Nachtigall, J Vondrasek, O Bludsky
The Journal of Physical Chemistry C 113 (19), 8412-8419, 2009
Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential …
K Berka, R Laskowski, KE Riley, P Hobza, J Vondrasek
Journal of Chemical Theory and Computation 5 (4), 982-992, 2009
Another role of proline: stabilization interactions in proteins and protein complexes concerning proline and tryptophane
L Biedermannova, KE Riley, K Berka, P Hobza, J Vondrasek
Physical Chemistry Chemical Physics 10 (42), 6350-6359, 2008
Performance of the DFT-D method, paired with the PCM implicit solvation model, for the computation of interaction energies of solvated complexes of biological interest
KE Riley, J Vondrášek, P Hobza
Physical Chemistry Chemical Physics 9 (41), 5555-5560, 2007
Urea and guanidinium induced denaturation of a Trp-cage miniprotein
J Heyda, M Kožíšek, L Bednárova, G Thompson, J Konvalinka, ...
The Journal of Physical Chemistry B 115 (28), 8910-8924, 2011
Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides The Alanine Dipeptide Case Study
J Vymetal, J Vondrášek
The Journal of Physical Chemistry B 114 (16), 5632-5642, 2010
Database of three-dimensional structures of HIV proteinases
J Vondrasek, CP van Buskirk, A Wlodawer
Nature Structural Biology 4 (1), 8-8, 1997
Sexual attraction in the silkworm moth: nature of binding of bombykol in pheromone binding protein—an ab initio study
V Klusák, Z Havlas, L Rulı́šek, J Vondrášek, A Svatoš
Chemistry & Biology 10 (4), 331-340, 2003
Like-charge guanidinium pairing from molecular dynamics and ab initio calculations
M Vazdar, J Vymetal, J Heyda, J Vondrasek, P Jungwirth
The Journal of Physical Chemistry A 115 (41), 11193-11201, 2011
Ion specific effects of sodium and potassium on the catalytic activity of HIV-1 protease
J Heyda, J Pokorná, L Vrbka, R Vácha, B Jagoda-Cwiklik, J Konvalinka, ...
Physical Chemistry Chemical Physics 11 (35), 7599-7604, 2009
Gyration-and inertia-tensor-based collective coordinates for metadynamics. Application on the conformational behavior of polyalanine peptides and Trp-cage folding
J Vymětal, J Vondrášek
The Journal of Physical Chemistry A 115 (41), 11455-11465, 2011
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