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| Description
| - Structure and dynamics of nucleic acids are determined by molecular interactions and electronic properties of nucleic acid bases. In-depth analysis of the molecular interactions in nucleic acids will be carried out using a wide range of modern computational techniques. The highest quality quantum chemical approaches will characterise the electronic properties of nucleobases including their tautomeric eqiulibria, hydrogen bonding, base stacking and cation binding. However, the gas phase studiesthemselves are not sufficient to understand the role of molecular interactions in DNA. To achieve this, the role of environment must be properly accounted for. Thus, nucleobases and their complexes will also be studied in polar environment using a variety of classical and quantum chemical approaches. In order to complete the research, molecular dynamics will be used to investigate the role of molecular interactions in DNA oligonucleotides and their complexes with drugs. (en)
- Struktura a dynamika nukleových kyselin (NK) je dána intermolekulárními interakcemi mezi komponenty NK a elektronovými vlastnostmi bází nukleových kyselin a cukrfosfátové páteře. Cílem projektu je studium těchto vlastností a interakcí s využitím celé škály nejmodernějších výpočetních technik. Pro studium vlastností izolovaných bází (včetně jejich tautomerů), párů bází vázaných vodíkovými vazbami a párů bází v patrovém uspořádání budou použity metody kvantové chemie na nejvyšší možné dostupné úrovni. Sebelepší výpočty ve vakuu však nemohou poskytnout kompletní obraz o chování NK in vivo, a tudíž je nezbytné zahrnout do našich studií i vliv okolního prostředí. Proto je náš projekt zaměřen rovněž na studium komplexů NK a jejich komponent s vodou, iontya léčivy s využitím jak kvantově-chemického, tak klasického (molekulová dynamika a mechanika) přístupu.
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| Title
| - Structure and dynamics of DNA nitrogeneous bases, base pairs, oligonucleotides and their complexes with water, ions and drugs (en)
- Struktura a dynamika bází, párů bází nukleových kyselin, oligonukleotidů a jejich komplexů s vodou, ionty a léčivy
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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...datumDodatniDoRIV
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| http://linked.open...i/cep/druhSouteze
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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...vai/cep/kategorie
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| http://linked.open.../cep/klicovaSlova
| - DNA; DNA bases; molecular dynamics; ab initio quantum chemical calculations; solvation (en)
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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...lneniVMinulemRoce
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| http://linked.open.../prideleniPodpory
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| http://linked.open...iciPoslednihoRoku
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| http://linked.open...atUdajeProjZameru
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| http://linked.open.../vavai/cep/soutez
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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...ep/ukonceniReseni
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| http://linked.open.../cep/vedlejsiObor
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| http://linked.open...ep/zahajeniReseni
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| http://linked.open...jektu+dodavatelem
| - Noncovalent interactions of nucleic acid bases and their role to structure, energetics, dynamic and properties of DNA were studied using a variety of state of the art computational methods. Pair interactions were described by accurate quantum chemical pr (en)
- Nekovalentní interakce bazí nukleových kyselin a jejich vliv na strukturu, energetiku, dynamiku a vlastnosti DNA byly studovány pomocí širokého spektra metod výpočetní chemie. Párové interakce byly popsány nejpřesnějšími metodami kvantové chemie a tento (cs)
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| http://linked.open...tniCyklusProjektu
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| http://linked.open.../cep/klicoveSlovo
| - DNA
- DNA bases
- ab initio quantum chemical calculations
- molecular dynamics
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| is http://linked.open...vavai/riv/projekt
of | - Principles of RNA base pairing: Structures and energies of the trans Watson-Crick/sugar edge base pairs
- Are the hydrogen bonds of RNA (.U) stronger than those of DNA (A.T)? A quantum mechanics study
- A DFT-D investigation of the mechanisms for activation of the wild-type and S810L mutated mineralocorticoid receptor by steroid hormones
- Correlation between the thermodynamic stability of DNA duplexes and the interaction and solvation energies of DNA building blocks
- Identifying stabilizing key residues in proteins using interresidue interaction energy matrix
- Bioinformatic analysis and molecular modelling of human ameloblastin suggest a two-domain intrinsically unstructured calcium-binding protein
- Representative amino acid side chain interactions in proteins. A comparison of highly accurate correlated ab initio quantum chemical and empirical potential procedures
- Analysis of Energy Stabilization inside the Hydrophobic Core of Rubredoxin
- Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA
- Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by Molecular Dynamics
- On differences between hydrogen bonding and improper blue-shifting hydrogen bonding
- Mutagenic properties of 5-halogenuracils: Correlated quantum chemical ab initio study
- Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: Complete basis set calculations at the MP2 a...
- Photochemical selectivity in guanine-cytosine base-pair structures
- Potential energy surfaces of an adenine-thymine base pair and its methylated analogue in the presence of one and two water molecules: Molecular mechanics and correlated ab initio study
- IR-UV double resonance spectroscopy of guanine-H2O clusters
- Hydration-induced changes of structure and vibrational frequencies of methylphosphocholine studied as a model of biomembrane lipids
- Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. Part. 4. Uracil and thymine
- The X3LYP extended density functional accuratelydescribes H-bonding but fails completely for stacking
- Hydration Gibbs energies of nucleic acid bases determined by Gibbs energy perturbation, continuous and hybrid approaches
- On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level
- Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family
- Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases
- Tautomeric Equilibrium, Stability, and Hydrogen Bonding in 2-Deoxyguanosine Monophosphate Complexed with Mg2+
- RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics
- Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations
- Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme
- Trapped water molecules are essential to structural dynamics and function of a ribozyme
- Molecular dynamics simulations of RNA: An in silico single molecule approach
- Binding of cationic and neutral phenanthridine intercalators to a DNA oligomer is controlled by the dispersion energy. Quantum chemical calculations and molecular mechanics simulations
- The world of non-covalent interactions: 2006
- Na+, Mg2+, and Zn2+ binding to all tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine: A correlated ab initio quantum chemical study
- Exceptional Thermodynamic Stability of DNA Duplexes Modified by Nonpolar Base Analogues Is due to Increased Stacking Interactions and Favorable Solvation: Correlated Ab Initio Calculations and Molecular Dynamics Simulations
- Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: Correlated ab initio quantum-chemical, DFT and empirical calculations
- Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs
- Theoretical investigations into the blue-shifting hydrogen bond in benzene complexes
- Theoretical study of the ground and excited states of 7-methyl guanine and 9-methyl guanine: comparison with experiment
- Interaction of heteroboranes with biomolecules, Part 2: The effect of various metal vertices and exo-substitutions
- Stabilisation energy of C6H6 ... C6X6 (X = F, Cl, Br, I, CN) complexes: complete basis set limit calculations at MP2 and CCSD(T) levels
- On the origin of red and blue shifts of X – H and C – H stretching vibrationsin formic acid (formate ion) and proton donor complexes
- Hydrogen-bonded nucleic acid base pairs containing unusual base tautomers: complete basis set calculations at the MP2 and CCSD(T) levels
- Gas-phase spectroscopy of biomolecular building blocks
- Benchmark RI-MP2 database of nucleic acid base trimers: performance of different density functional models for prediction of structures and binding energies
- The Mid-IR spectra of 9-ethyl guanine, guanosine, and 2-deoxyguanosine
- Leading RNA tertiary interactions: Structures, energies, and water insertion of a-minor and P-interactions. A quantum chemical view
- On the nature of DNA - duplex stability
- Density-functional, density-functional tight-binding, and wave-function calculations on biomolecular systems
- Model of peptide bond - aromatic ring interaction: correlated ab initio quantum chemical study
- DNA base trimers: empirical and quantum chemical ab initio calculations
- Stability of nucleic acid base pairs in organic solvents: Molecular dynamics, molecular dynamics/quenching, and correlated ab initio study
- Hydration and stability of nucleic acid bases and base pairs
- Density functional theory-symmetry adapted perturbation treatment energy decomposition of nucleic acid base pairs taken from DNA crystal geometry
- Non-covalent interactions in biomacromolecules
- Assessment of the MP2 method, along with several basis sets, for the computation of interaction energies of biologically relevant hydrogen bonded and dispersion bound complexes
- C-H stretching vibrational shift of benzene dimer: Consistency of experiment and calculation
- Structural and evolutionary classification of G/U wobble basepairs in the ribosome
- Molecular dynamics simulations of sarcin-ricin rRNA motif
- Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps
- Mechanism of action of anticancer titanocene derivatives: An insight from quantum chemical calculations
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