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	Structure-activity relationship of glutamate carboxypeptidase II Navrátil, Václav ; Konvalinka, Jan (advisor) ; Burda, Jaroslav (referee) Detailed record
	Theoretical Studies of Ligand Fields Influence on Physico-Chemical Behavior of Copper Cations Cu(I)/Cu(II) Pavelka, Matěj ; Burda, Jaroslav (advisor) ; Rulíšek, Lubomír (referee) ; Koča, Jaroslav (referee) Detailed record
	MD simulations of complexes consisted of HIV reverse transcriptase and its potental inhibitors Saralamba, Sompob ; Barvík, Ivan (advisor) ; Burda, Jaroslav (referee) Detailed record
	Computational Study of the Reaction Mechanisms of the Interaction of Nukleobases with Dirhodium Complexes active in Anticancer treatment by quantum chemical methods. Golan, Martin ; Burda, Jaroslav (advisor) ; Sochorová Vokáčová, Zuzana (referee) Detailed record
	Theoretical study of cisplatin analogs using ab initio quantum chemistry methods Zeizinger, Michal ; Burda, Jaroslav (advisor) ; Urban, Ján (referee) ; Šponer, Judit E. (referee) Detailed record
	Quantum chemical study of the electron properties of various platinum complexes Michera, Luděk ; Burda, Jaroslav (advisor) ; Sychrovský, Vladimír (referee) Detailed record
	Combined QM/MM decsription of interaction of Ru(II) 'piano-stool' organometallic complexes with oligomer models of DNA Zábojníková, Tereza ; Burda, Jaroslav (advisor) ; Sychrovský, Vladimír (referee) This work is focused on 4 organometalic drugs with "piano-stool" Ru(II) structure: these complexes are: nalidixic acid, thio-nalidixic acid, ofloxacin and cinoxacin. Thermodynamic parameters of three type of reactions with water were analyzed for each of these four complexes. All complexes were examined in both protonated and deprotonated state, since all of these complexes are acids and they behave differently in acidic and neutral enviroment. Optimalization was performed using DFT method B3PW91 in basis 6-31+G*. Energies were calculated in basis 6-311++G(2df,2pd) using DFT method B3LYP and NPA analysis was performed for finding partial charges on atoms. Detailed record
	Theoretical studies of the ruthenium complexes with anticancer activities. Futera, Zdeněk ; Burda, Jaroslav (advisor) ; Šponerová, Judit (referee) Detailed record
	Noncovalent Interactions in the Gas Phase and Aqueous Solution: Theoretical Study Zendlová, Lucie ; Hobza, Pavel (advisor) ; Burda, Jaroslav (referee) ; Vondrášek, Jiří (referee) ; Jurečka, Petr (referee) EAPUr rr\|lclltal \ alLlť5' 5 Conclusions :, , . In the ia) part of present work we c intera cti on b etween u d"',il ". . . thy;';; il:'::: :íJTj.:lÍ' lI jl.#.ffiJ,lil itt8:"é'siia small number oru.",7nJ organió solvent ňr"."i", (CH3.H, solvents yů[T"i^f.completely different interactions between the bases and the b"''" p.'"{ ;' "idilnn il#} il-t ÍT:!fl,-. i: : " o:] Y" .'h:.-S,t. tu,", ot tt," moleóule Iuórc 'u'r' u property, and the'. .'l,'..,ťff,.'lt'Lť':.lill:ilF.S'T!,l;situated above or belolthe !Á; ;;i. ;';;lě'"o ri," olašó ň"l"-.\,," ,, unique y"J::fiffii:x::. ."n'oison with otr,!. .otu"nt,, uň.'r,"í'ř;;.". are the In the ib) part_of present work based on the MD, SCC_DDFTB_D and ;"",'.Y\|Tť'.#1.:."ffi i"T."lrJ'".r""u.'".XincorporateJ."-oŇTduplexwe i) Replacing nucleic acid base by modified nucleobase X leads.:'] ,o Structural changes of the centrď -uuš"-pui. Gtu.tarrangement of central modified base pairs). ónli with ttresma'lest modified nucleobase p 'r'" Á.iJ.;;;;.í' (A-P, P-T) stay planar. In the case 'of.B-T, Á-il.;';6 in specificorientation, one of the modified nuú"JÁ""x"íto.""a outfrom DNA duplex. ii) Incre, .,""olr'iT"i1iTi1fi" or modified nucleobase X increases rhe iii) The highest s.ďectivity among- all base ana\|ogue studied wasfound for modified nu"l"obus" O In the secono pu of... Detailed record
	Interaction of Metal Cations in Bioorganic Environment. Computational Study Using Quantum Mechanics and Molecular MechanicsTools. Futera, Zdeněk ; Burda, Jaroslav (advisor) ; Bouř, Petr (referee) ; Clark, Tim (referee) Interactions of Metal Cations in Bioorganic Environment Computational Study Using Quantum Mechanics and Molecular Mechanics Tools Zdeněk Futera Biologically relevant interactions of piano-stool ruthenium(II) complexes with ds-DNA are studied by QM/MM computational technique. The whole re- action mechanism is divided into three phases - hydration of [RuII (η6 - benzene)(en)Cl]+ , consequent binding DNA and final intra-strand cross-link formation between two adjacent guanines. Free energy profiles of all reactions are explored by QM/MM MD umbrella sampling approach where the Ru(II) complex is described by DFT. For that purpose, special QM/MM software was developed to couple Gaussian and Amber programs. Calculated free energy barriers of Ru(II) hydration as well as DNA binding process are in good agreement with experimentally determined rate constants. Reaction pathway for cross-link formation was predicted that is feasible from both thermodynamical and kinetical point of view. Detailed record

See also: similar author names
3	BURDA, Jakub
3	BURDA, Jiří
3	Burda, Jakub
14	Burda, Jan
3	Burda, Jiří
1	Burda, Josef

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