Search Results - "Jurečka, Petr"

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview by Šponer, Jiří, Bussi, Giovanni, Krepl, Miroslav, Banáš, Pavel, Bottaro, Sandro, Cunha, Richard A, Gil-Ley, Alejandro, Pinamonti, Giovanni, Poblete, Simón, Jurečka, Petr, Walter, Nils G, Otyepka, Michal

“…With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are…”
Get full text

Noncovalent Interactions by Quantum Monte Carlo by Dubecký, Matúš, Mitas, Lubos, Jurečka, Petr

“…Quantum Monte Carlo (QMC) is a family of stochastic methods for solving quantum many-body problems such as the stationary Schrödinger equation. The review…”
Get full text

Assessing the Current State of Amber Force Field Modifications for DNA by Galindo-Murillo, Rodrigo, Robertson, James C, Zgarbová, Marie, Šponer, Jiří, Otyepka, Michal, Jurečka, Petr, Cheatham, Thomas E

“…The utility of molecular dynamics (MD) simulations to model biomolecular structure, dynamics, and interactions has witnessed enormous advances in recent years…”
Get full text

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B‑DNA by Zgarbová, Marie, Šponer, Jiří, Otyepka, Michal, Cheatham, Thomas E., Galindo-Murillo, Rodrigo, Jurečka, Petr

“…Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations…”
Get full text

Adsorption of Small Organic Molecules on Graphene by Lazar, Petr, Karlický, František, Jurečka, Petr, Kocman, Mikuláš, Otyepková, Eva, Šafářová, Klára, Otyepka, Michal

“…We present a combined experimental and theoretical quantification of the adsorption enthalpies of seven organic molecules (acetone, acetonitrile,…”
Get full text

Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories by Riley, Kevin E, Pitoňák, Michal, Jurečka, Petr, Hobza, Pavel

“…Riley et al discuss the stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density…”
Get full text

Z‑DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER by Zgarbová, Marie, Šponer, Jiří, Jurečka, Petr

“…Although current AMBER force fields are relatively accurate for canonical B-DNA, many noncanonical structures are still described incorrectly. As noncanonical…”
Get full text

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles by Zgarbová, Marie, Otyepka, Michal, Šponer, Jiří, Mládek, Arnošt, Banáš, Pavel, Cheatham, Thomas E, Jurečka, Petr

“…We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force field for RNA, χOL. The parameters remove destabilization of the…”
Get full text

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA by Zgarbová, Marie, Otyepka, Michal, Šponer, Jiří, Lankaš, Filip, Jurečka, Petr

“…Terminal base pairs of DNA and RNA molecules in solution are known to undergo frequent transient opening events (fraying). Accurate modeling of this process is…”
Get full text

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters by Zgarbová, Marie, Luque, F. Javier, Šponer, Jiří, Cheatham, Thomas E, Otyepka, Michal, Jurečka, Petr

“…We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as…”
Get full text

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins by Banáš, Pavel, Hollas, Daniel, Zgarbová, Marie, Jurečka, Petr, Orozco, Modesto, Cheatham, Thomas E, Šponer, Jiří, Otyepka, Michal

“…The RNA hairpin loops represent important RNA topologies with indispensable biological functions in RNA folding and tertiary interactions. 5′-UNCG-3′ and…”
Get full text

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome by Šponer, Jiří, Banáš, Pavel, Jurečka, Petr, Zgarbová, Marie, Kührová, Petra, Havrila, Marek, Krepl, Miroslav, Stadlbauer, Petr, Otyepka, Michal

“…We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the…”
Get full text

True Stabilization Energies for the Optimal Planar Hydrogen-Bonded and Stacked Structures of Guanine···Cytosine, Adenine···Thymine, and Their 9- and 1-Methyl Derivatives:  Complete Basis Set Calculations at the MP2 and CCSD(T) Levels and Comparison with Experiment by Jurečka, Petr, Hobza, Pavel

“…Planar H-bonded and stacked structures of guanine···cytosine (G···C), adenine···thymine (A···T), 9-methylguanine···1-methylcytosine (mG···mC), and…”
Get full text

Understanding of Assembly Phenomena by Aromatic−Aromatic Interactions:  Benzene Dimer and the Substituted Systems by Lee, Eun Cheol, Kim, Dongwook, Jurečka, Petr, Tarakeshwar, P, Hobza, Pavel, Kim, Kwang S

“…Interactions involving aromatic rings are important in molecular/biomolecular assembly and engineering. As a consequence, there have been a number of…”
Get full text

Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs by Šponer, Jiří, Jurečka, Petr, Hobza, Pavel

“…Hydrogen-bonded nucleic acids base pairs substantially contribute to the structure and stability of nucleic acids. The study presents reference ab initio…”
Get full text

Assessing the Current State of Amber Force Field Modifications for DNA2023 Edition by Love, Olivia, Galindo-Murillo, Rodrigo, Zgarbová, Marie, Šponer, Jiří, Jurečka, Petr, Cheatham, Thomas E.

“…Advances in molecular dynamics (MD) software alongside enhanced computational power and hardware have allowed for MD simulations to significantly expand our…”
Get full text

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 by Jurecka, Petr, Sponer, Jirí, Cerný, Jirí, Hobza, Pavel

“…MP2 and CCSD(T) complete basis set (CBS) limit interaction energies and geometries for more than 100 DNA base pairs, amino acid pairs and model complexes are…”
Get more information

A- to B‑DNA Transition in AMBER Force Fields and Its Coupling to Sugar Pucker by Zgarbová, Marie, Jurečka, Petr, Šponer, Jiří, Otyepka, Michal

“…The A/B transition is a basic element of DNA conformational change. Because of its involvement in the sensing of the ionic conditions by DNA and in specific…”
Get full text

Toward Accurate Hydrogen Bonds by Scalable Quantum Monte Carlo by Dubecký, Matúš, Jurečka, Petr, Mitas, Lubos, Ditte, Matej, Fanta, Roman

“…Single-determinant (SD) fixed-node diffusion Monte Carlo (FNDMC) gains popularity as a benchmark method scalable to large noncovalent systems, although its…”
Get full text

Quantum Monte Carlo Methods Describe Noncovalent Interactions with Subchemical Accuracy by Dubecký, Matúš, Jurečka, Petr, Derian, René, Hobza, Pavel, Otyepka, Michal, Mitas, Lubos

“…An accurate description of noncovalent interaction energies is one of the most challenging tasks in computational chemistry. To date, nonempirical CCSD(T)/CBS…”
Get full text