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Journal of Chemical Theory and Computation, ISSN 1549-9618, 07/2015, Volume 11, Issue 8, pp. 3866 - 3877
RNA hairpins capped by 5'-GNRA-3' or 5'-UNCG-3' tetraloops (TLs) are prominent RNA structural motifs. Despite their small size, a wealth of experimental data,... 
Nucleic Acid Denaturation | Proteins - metabolism | Hydrogen Bonding | Base Sequence | Proteins - chemistry | Nucleic Acid Conformation | RNA - chemistry | Molecular Dynamics Simulation | Computer simulation | Ribonucleic acids | Molecular dynamics | Mathematical models | Sampling | Chemical vapor synthesis | Folding | Standards
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 01/2014, Volume 10, Issue 1, pp. 401 - 411
Hydrating water molecules are believed to be an inherent part of the RNA structure and have a considerable impact on RNA conformation. However, the magnitude... 
BIOMOLECULAR SIMULATIONS | AMBER FORCE-FIELD | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | LIQUID WATER | CHEMISTRY, PHYSICAL | POTENTIAL FUNCTIONS | SOLVATION DYNAMICS | B-DNA | RIBOSOMAL-RNA | CHARGE MODEL | NUCLEIC-ACIDS | AQUEOUS-SOLUTION
Journal Article
The Journal of Physical Chemistry B, ISSN 1520-6106, 03/2015, Volume 119, Issue 11, pp. 4220 - 4229
X-ray crystallography can provide important insights into the structure of RNA enzymes (ribozymes). However, the details of a ribozyme’s active site... 
Protons | Catalytic Domain | DNA - chemistry | Quantum Theory | RNA, Catalytic - metabolism | Phosphates - chemistry | Crystallography, X-Ray | Ribose - chemistry | DNA - metabolism | RNA, Catalytic - chemistry | Molecular Dynamics Simulation
Journal Article
The Journal of Physical Chemistry B, ISSN 1520-6106, 12/2017, Volume 121, Issue 48, pp. 10828 - 10840
Ribozymes utilize diverse catalytic strategies. We report systematic quantum chemical calculations mapping the catalytic space of RNA cleavage by comparing all... 
2'-HYDROXYL GROUP | ACID-BASE CATALYSIS | MOLECULAR-DYNAMICS | GLMS RIBOZYME | ACTIVE-SITE | CRYSTAL-STRUCTURE | CHEMISTRY, PHYSICAL | SELF-CLEAVING RIBOZYMES | DELTA-VIRUS RIBOZYME | HAMMERHEAD-RIBOZYME | HAIRPIN RIBOZYME | Usage | Molecular computing | Catalytic RNA | Analysis | Chemical reactions | Research | Electrostatics
Journal Article
The Journal of Physical Chemistry Letters, ISSN 1948-7185, 05/2014, Volume 5, Issue 10, pp. 1771 - 1782
We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the... 
MATERIALS SCIENCE, MULTIDISCIPLINARY | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | NANOSCIENCE & NANOTECHNOLOGY | EXPLICIT SOLVENT | AMBER FORCE-FIELD | QUADRUPLEX DNA | REPLICA-EXCHANGE METHOD | TRANSFER-RNA | HDV RIBOZYME | BINDING-SITES | DELTA-VIRUS RIBOZYME | ENERGY LANDSCAPE | STRUCTURAL DYNAMICS
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 08/2019, Volume 47, Issue 14, pp. 7276 - 7293
Abstract Guanine quadruplexes (G4s) are non-canonical nucleic acids structures common in important genomic regions. Parallel-stranded G4 folds are the most... 
SINGLE-MOLECULE FRET | TELOMERIC G-QUADRUPLEX | AMBER FORCE-FIELD | MONOVALENT ION PARAMETERS | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | REPLICA-EXCHANGE | PARTICLE MESH EWALD | K+ SOLUTION | ENERGY LANDSCAPE | NUCLEIC-ACIDS | Computational Biology
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 04/2013, Volume 9, Issue 4, pp. 2115 - 2125
RNA hairpin loops represent important RNA motifs with indispensable biological functions in RNA folding and tertiary interactions, with the 5′-UNCG-3′ and... 
ANGSTROM RESOLUTION | TERTIARY INTERACTIONS | CRYSTAL-STRUCTURE | DNA HAIRPIN | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | FORCE-FIELD | MOLECULAR-DYNAMICS SIMULATIONS | SARCIN RICIN LOOP | RIBOSOMAL-RNA | ENERGY LANDSCAPE | NUCLEIC-ACIDS
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 05/2019, Volume 15, Issue 5, pp. 3288 - 3305
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 09/2018, Volume 46, Issue 17, pp. 8754 - 8771
Journal Article
NATURE COMMUNICATIONS, ISSN 2041-1723, 09/2019, Volume 10, Issue 1, pp. 1 - 16
The widespread Mn2+-sensing yybP-ykoY riboswitch controls the expression of bacterial Mn2+ homeostasis genes. Here, we first determine the crystal structure of... 
HETEROGENEITY | MOLECULAR-DYNAMICS | MECHANICS | SINGLE | RNA STRUCTURE | EUBACTERIA SENSE | MULTIDISCIPLINARY SCIENCES | SIMULATIONS | PARAMETERS | BINDING | REVEALS | Adenosine | Core loss | Homeostasis | Ribonucleic acid--RNA | Gene expression | Signal transduction | Aptamers | Ligands | Transduction | Fluorescence resonance energy transfer | Magnesium | Mutation | Crystal structure | Conformation | Metal ions
Journal Article