| 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 | 963 | 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 | 471 | 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 | 324 | 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 | 272 | 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 | 222 | 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 | 188 | 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 | 186 | 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 | 178 | 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 | 165 | 2008 |
| The LOTUS initiative for open knowledge management in natural products research A Rutz, M Sorokina, J Galgonek, D Mietchen, E Willighagen, A Gaudry, ... Elife 11, e70780, 2022 | 129 | 2022 |
| 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 | 122 | 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 | 104 | 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 | 98 | 2008 |
| Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides The Alanine Dipeptide Case Study J Vymetal, J Vondrasek The Journal of Physical Chemistry B 114 (16), 5632-5642, 2010 | 82 | 2010 |
| 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 | 79 | 2007 |
| Random protein sequences can form defined secondary structures and are well-tolerated in vivo V Tretyachenko, J Vymětal, L Bednárová, V Kopecký Jr, K Hofbauerová, ... Scientific Reports 7 (1), 15449, 2017 | 73 | 2017 |
| 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 | 71 | 2011 |
| 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 | 66 | 2011 |
| Database of three-dimensional structures of HIV proteinases. J Vondrasek, CP Buskirk, A Wlodawer | 65 | 1997 |
| Gyration-and inertia-tensor-based collective coordinates for metadynamics. Application on the conformational behavior of polyalanine peptides and Trp-cage folding J Vymetal, J Vondrášek The Journal of Physical Chemistry A 115 (41), 11455-11465, 2011 | 64 | 2011 |
