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Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM
Hybrid QM/MM methods combine the rigor of quantum mechanical (QM) calculations. Catalysis by RNA enzymes (ribozymes) has only recently begun to be addressed with QM/MM as well as recent advances in QM<...
CF - Fyzikální chemie a teoretická chemie
- 2009 •
- Jx
Rok uplatnění
Jx - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)
Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes
continuum solvent QM and explicit solvent QM/MM optimizations. We report geometry geometries. In QM/MM, the initial solvent configuration causes some heterogeneity differences in the relative energies of ...
BO - Biofyzika
- 2016 •
- Jx •
- Link
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Jx - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)
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A double-QM/MM method for investigating donor-acceptor electron-transfer reactions in solution
We developed a double-quantum mechanical/molecular mechanical (d-QM/MM) method and an acceptor (DA) in condensed matter. In the d-QM/MM method, which employs the novel reactions, and demonstrated that the d-QM<...
BJ - Termodynamika
- 2014 •
- Jx •
- Link
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Jx - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)
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Quantum Mechanical Scoring: Structural and Energetic Insights into Cyclin-Dependent Kinase 2 Inhibition by Pyrazolo[1,5-a]pyrimidines
inhibitors and their bioisosteres. A hybrid three-layer QM/MM setup (DFT-D/PM6-D3H4X of our previous full QM and SQM/MM (SQM means semiempirical QM) approaches. Two a QM/SQM/MM optimizat...
CF - Fyzikální chemie a teoretická chemie
- 2013 •
- Jx
Rok uplatnění
Jx - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)
A combined quantum and molecular mechanical study of the O2 reductive cleavage in the catalytic cycle of multicopper oxidases
Using QM/MM calculations, the key intermediates of the reaction cycle of multicopper oxidases have been structurally characterized and the reaction mechanism proposed....
CF - Fyzikální chemie a teoretická chemie
- 2005 •
- Jx
Rok uplatnění
Jx - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)
QM/MM Calculations on Protein-RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods
structures. Herein, we report a series of large-scale QM/MM calculations on the U1A protein-RNA interface, which is very unstable in MD simulations. The QM/MM that advanced QM/MM computations cou...
Physical chemistry
- 2018 •
- Jimp •
- Link
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Jimp - Článek v periodiku v databázi Web of Science
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Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions
-energy calculation methods: molecular mechanics/Poisson-Boltzmann surface area (MM/ PBSA), MM/generalized Born surface area (MM/GBSA), and quantum mechanics-MM/GBSA (QM-MM/GBSA) on monosaccharide...
Physical chemistry
- 2018 •
- Jimp •
- Link
Rok uplatnění
Jimp - Článek v periodiku v databázi Web of Science
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Predicting Effects of Site-Directed Mutagenesis on Enzyme Kinetics by QM/MM and QM Calculations: A Case of Glutamate Carboxypeptidase II
Quantum and molecular mechanics (QM/MM) and QM-only (cluster model) modeling. One of the stringent tests for QM/MM and/or QM approaches is to provide calculated by QM/MM and ...
Physical chemistry
- 2022 •
- Jimp •
- Link
Rok uplatnění
Jimp - Článek v periodiku v databázi Web of Science
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On the Association of the Base Pairs on the Silica Surface Based on Free Energy Biased Molecular Dynamics Simulation and Quantum Mechanical Calculations
calculations. The MM interaction energies for all clusters agreed well with the QM ones are adsorbed on a fully solvated silica surface in different H-bonded forms. Both QM and MM surface has been investigated by ...
CF - Fyzikální chemie a teoretická chemie
- 2013 •
- Jx •
- Link
Rok uplatnění
Jx - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)
Výsledek na webu
Reduction Potentials and Acidity Constants of Mn Superoxide Dismutase Calculated by QM/MM Free-Energy Methods
and molecular mechanics (QM/MM) thermodynamic cycle perturbation (QTCP) and the QM/MM-PBSA approach. In the latter, QM/MM energies are combined with continuum solvation energies more positive pot...
CF - Fyzikální chemie a teoretická chemie
- 2011 •
- Jx •
- Link
Rok uplatnění
Jx - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)
Výsledek na webu
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