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| Description
| - The aim of the project is to understand structural flexibility of the DNA molecule and its internal dynamics by combining ab initio quantum chemical calculations, vibrational dynamics, and analyses of the crystallographic structural databases. Structure and dynamics of the DNA bases, and their hydrogen bonded and stacked pairs will be characterized by ab initio calculations. The obtained characteristics will be used to rationalize the internal dynamics of the bases so that we sill able to explain the observed conformational variability of the DNA molecule. These characteristics will be also used for testing and/or reparametrization of empirical potentials. The DNA backbone structural variability will be studied by a systematic analysis of the structural databases and by ab initio calculations, and results will be correlated to the DNA conformations experimentally observed in DNA - protein complexes. (en)
- Strukturní flexibilita a vnitřní dynamika molekuly DNA bude studována pomocí ab initio kvantověchemických výpočtů, vibrační dynamiky a analýzy krystalových databázových struktur. Strukturní a dynamické charakteristiky bází DNA a jejich párů s vodíkovou vazbou, jakož i patrových párů, budou určeny pomocí ab initio výpočtů. Získané charakteristiky budou použity při racionalizaci vnitřní dynamiky párů a povedou k interpretaci konformační variability DNA. Strukturní variabilita páteře DNA bude studována pomocí systematické analýzy krystalových databází a ab initio výpočtů a výsledky budou korelovány s konformacemi DNA pozorovanými v komplexech DNA - bílkovina.
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| Title
| - Structure and dynamics of DNA (en)
- Struktura a dynamika DNA
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| skos:notation
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| http://linked.open...avai/cep/aktivita
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| http://linked.open...kovaStatniPodpora
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| http://linked.open...ep/celkoveNaklady
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| http://linked.open...ep/duvernostUdaju
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| http://linked.open.../cep/fazeProjektu
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| http://linked.open...ai/cep/hlavniObor
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| http://linked.open...hodnoceniProjektu
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| http://linked.open...ep/partnetrHlavni
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| http://linked.open...inujicichPrijemcu
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| http://linked.open...cep/pocetPrijemcu
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| http://linked.open...ocetSpoluPrijemcu
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| http://linked.open.../pocetVysledkuRIV
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| http://linked.open...enychVysledkuVRIV
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| http://linked.open...iciPoslednihoRoku
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| http://linked.open...atUdajeProjZameru
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| http://linked.open...usZobrazovaneFaze
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| http://linked.open...ai/cep/typPojektu
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| http://linked.open.../cep/vedlejsiObor
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| http://linked.open...jektu+dodavatelem
| - Hodnocený projekt se zabýval nesmírně důležitou tématikou interakce bází nukleových kyselin s ionty kovů. Projekt byl připraven i vyřešen vynikajícím způsobem. Autoři dosáhli zásadních výsledků, které publikovali v renomovaných časopisech (celkem 31 člán (cs)
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| http://linked.open...tniCyklusProjektu
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| is http://linked.open...vavai/riv/projekt
of | - Hydrogen-bonded Trimers of DNA Bases and their Interaction with Metal Cations: Ab initio Quantum-chemical and Empirical Potential Study.
- 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 Interaction of DNA Bases:Comparison with Nonempirical Beyond Hartree-Fock Results.
- Thioguanine and Thiouracil: Hydrogen-Bonding and Stacking Properties.
- Thioguanine and Thiouracil: Hydrogen-Bonding and Stacking Propeties.
- Molecular dynamics of hemiprotonated intercalated four-stranded i-DNA: stable trajectories on a nanosecond scale
- Reverse Watson-Crick Isocytosine-Cytosine and Guanine-Cytosine Base Pairs Stabilized by the Formation of the Minor Tautomers of Bases. An ab initio Study in the Gas Phase and in a Water Cluster.
- Uracil Dimer: Potential Energy and Free Energy Surfaces. Ab initio beyond Hartee-Fock and Empirical Potential Studies.
- Computational Approaches to the Studies of the Interactions of Nucleic Acid Bases.
- Crystal Structure of d(GGCCAATTGG) Complexed with DAPI Reveals Novel Binding Mode.
- Complexes of Pentahydrated Zn 2+ with Guanine, Adenine, and the Guanine-Cytosine and Adenine-Thymine Base-Pairs. Structures and Energies Characterized by Polarizable Molecular Mechanics and ab initio Calculations.
- Complexes of Pentahydrated ZN .sup.2+ with Guanine, Adenine, and Guanine-Cytosina and Adenine-Thymine Base Pairs. Structure and Energies Characterized by Polarizable Molecular Mechanics and ab Initio Calculations.
- Metal Ions in Non-complementary DNA Base Pairs: an ab initio Study of Cu(I), Ag(I), and Au(I) Complexes with the Cytosine-Adenine Base Pair.
- Thermodynamic Parameters for Stacking and Hydrogen Bonding of Nucleic Acid Bases in Aqueous Solution: Ab initio/Langevin Dipoles Study.
- Anti-Hydrogen Bond in the Benzene Dimer and Other Carbon Proton Donor Complexes.
- A Quantum Chemical ab initio Study of the Interaction between CO + and Ni + Ions with CO 2 and N 2 O.
- Structure, Energetics, Vibrational Frequencies and Charge Transfer of Base Pairs, Nucleoside Pairs, Nucleotide Pairs and B-DNA Pairs of Trinucleotides: ab initio HF/MINI-1 and Empirical Force Field Study.
- Interaction between the Guanine-Cytosine Watson-Crick DNA Base Pair and Hydrated Group IIa (Mg 2+ , Ca 2+ , Sr 2+ , Ba 2+ ) and IIb (Zn 2+ , Cd 2+ , Hg 2+ ) Metal Cations.
- Nuclear Dynamics of Benzene.lmbd..lmbd..lmbd.(Ar) n Clusters.
- On the Potential Role of the Amino Nitrogen Atom as a Hydrogen Bond Acceptor in Macromolecules.
- Stabilization of the Purine.Purine.Pyrimidine DNA Base Triplets by Divalent Metal Cations.
- Significant Structural Deformation of Nucleic Acid Bases in Stacked Base Pairs: an ab initio Study beyond Hartree-Fock.
- Stabilization of the Purine.lmbd.Purine.lmbd.Pyrimidine DNA Base Triplets by Divalent Metal Cations.
- Anti-hydrogen Bond between Chloroform and Fluorobenzene.
- Benzene Trimer and Benzene Tetramer: Structures and Properties Determined by the Nonempirical Model (NEMO) Potential Calibrated from the CCSD(T) Benzene Dimer Energies.
- Adenine...2,4-Difluorotoluene (Modified Base) Pair: Potential and Free-Energy Surfaces. Non-empirical and Empirical Potential Studies.
- Interaction of the Adenine-Thymine Watson-Crick and Adenine-Adenine Reverse-Hoogsteen DNA Base Pairs with Hydrated Group IIa (Mg .sup.2+, Ca .sup.2+, Sr .sup.2+, Ba .sup.2+) and IIb (Zn .sup.2+, Cd .sup.2+, Hg .sup.2+) Metal Cations: Absence of the Base
- Interaction of the Adenine-Thymine Watson-Crick and Adenine-Adenine Reverse-Hoogsteen DNA Base Pairs with Hydrated Group IIa (Mg 2+ , Ca 2+ , Sr 2+ , Ba 2+ ) and IIb (Zn 2+ , Cd 2+ , Hg 2+ ) Metal Cations:Absence of the Base Pair Stabilization by Metal-I
- Interactions of Hydrated IIa and IIb Group Metal Cations with Thioguanine-Cytosine DNA Base Pair: Ab initio and Density Functional Theory Investigation of Polarization Effects, Differences Among Cations, and Flexibility of the Cation Hydration Shell.
- Nanosecond molecular dynamics simulations of parallel and antiparallel guanine quadruplex DNA molecules
- Structure and Vibrational Dynamics of the Benzene Dimer.
- Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical ab initio Calculations.
- De novo acute myeloid leukemias with normal cytogenetics involve two main prognosticcategories distinguished by the presence of erythroblastic and/or megacaryocytic dysplasia?
- Erythroblastic and/or megakaryocytic dysplasia in de novo acute myeloid leukemias M0-M5 show relation to myelodysplastic syndromes and delimit two main categories.
- FTIR Spectro-photoelectrochemical Cell with Adjustable Solutin Layer Thickness. Photocurrent Transients at Photoexcited TiO 2 Polycrystalline Electrodes.
- Accurate ab initio Calculations on Large van der Waals Clusters.
- Base-Base and Deoxyribose-Base Stacking Interactions in B-DNA and Z-DNA: a Quantumm-Chemical Study.
- Anharmonic and Harmonic Intermolecular Vibrational Modes of the DNA Base Pairs.
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| is http://linked.open...vavai/cep/projekt
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