The role of an active site Mg2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

(2014) Vojtěch Mlýnský et al.   Journal of Chemical Theory and Computation

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

(2014) Jiří Šponer et al.   Journal of Physical Chemistry Letters

Quantum Mechanical/Molecular Mechanical Free Energy Simulations of the Self-Cleavage Reaction in the Hepatitis Delta Virus Ribozyme

(2014) Abir Ganguly et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

(2014) K. N. Sripathi et al.   RNA

Thio Effects and an Unconventional Metal Ion Rescue in the Genomic Hepatitis Delta Virus Ribozyme

(2013) Pallavi Thaplyal et al.   BIOCHEMISTRY

Computer Folding of RNA Tetraloops? Are We There Yet?

(2013) Petra Kührová et al.   Journal of Chemical Theory and Computation

Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration

(2012) Ivana Beššeová et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Mechanism of preQ1 Riboswitch Action: A Molecular Dynamics Study

(2012) Pavel Banáš et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Two Distinct Catalytic Strategies in the Hepatitis Delta Virus Ribozyme Cleavage Reaction

(2011) Barbara L. Golden   BIOCHEMISTRY

Metal Binding Motif in the Active Site of the HDV Ribozyme Binds Divalent and Monovalent Ions

(2011) Narayanan Veeraraghavan et al.   BIOCHEMISTRY

Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs

(2011) Petr Sklenovský et al.   Journal of Chemical Theory and Computation

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms

(2011) Vojtěch Mlýnský et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantum Mechanical/Molecular Mechanical Study of the HDV Ribozyme: Impact of the Catalytic Metal Ion on the Mechanism

(2011) Abir Ganguly et al.   Journal of Physical Chemistry Letters

A 1.9 Å Crystal Structure of the HDV Ribozyme Precleavage Suggests both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage

(2010) Jui-Hui Chen et al.   BIOCHEMISTRY

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

(2010) Pavel Banáš et al.   Journal of Chemical Theory and Computation

Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In

(2009) Mark A. Ditzler et al.   ACCOUNTS OF CHEMICAL RESEARCH

Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM

(2009) Pavel Banáš et al.   METHODS

General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility

(2008) Pavel Banáš et al.   JOURNAL OF PHYSICAL CHEMISTRY B