RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
CHARMM‐GUI 10 years for biomolecular modeling and simulation
CHARMM‐GUI, http://www. charmm-gui. org, is a web‐based graphical user interface that
prepares complex biomolecular systems for molecular simulations. CHARMM‐GUI creates …
prepares complex biomolecular systems for molecular simulations. CHARMM‐GUI creates …
An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations
A method is presented for the efficient evaluation of long-range electrostatic forces in
combined quantum mechanical and molecular mechanical (QM/MM) calculations of periodic …
combined quantum mechanical and molecular mechanical (QM/MM) calculations of periodic …
Development of range-corrected deep learning potentials for fast, accurate quantum mechanical/molecular mechanical simulations of chemical reactions in solution
We develop a new deep potential─ range correction (DPRc) machine learning potential for
combined quantum mechanical/molecular mechanical (QM/MM) simulations of chemical …
combined quantum mechanical/molecular mechanical (QM/MM) simulations of chemical …
Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms
A semiempirical AM1/d Hamiltonian is developed to model phosphoryl transfer reactions
catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined …
catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined …
Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent PO or PS bond dissociation
Iodine-induced cleavage at phosphorothioate DNA (PT-DNA) is characterized by extremely
high sensitivity (∼ 1 phosphorothioate link per 106 nucleotides), which has been used for …
high sensitivity (∼ 1 phosphorothioate link per 106 nucleotides), which has been used for …
Target-related applications of first principles quantum chemical methods in drug design
A fundamental postulate in the classical drug design paradigm is that the effect of a drug in
the human body is a consequence of the molecular recognition between a ligand (the drug) …
the human body is a consequence of the molecular recognition between a ligand (the drug) …
Unveiling the sulfur–sulfur bridge: Accurate structural and energetic characterization of a homochalcogen intermolecular bond
DA Obenchain, L Spada, S Alessandrini… - Angewandte Chemie …, 2018 - Wiley Online Library
By combining rotational spectroscopy in supersonic expansion with the capability of state‐of‐
the‐art quantum‐chemical computations in accurately determining structural and energetic …
the‐art quantum‐chemical computations in accurately determining structural and energetic …
Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis
The molecular mechanism of hairpin ribozyme catalysis is studied with molecular dynamics
simulations using a combined quantum mechanical and molecular mechanical (QM/MM) …
simulations using a combined quantum mechanical and molecular mechanical (QM/MM) …
Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation
TJ Giese, DM York - Journal of chemical theory and computation, 2016 - ACS Publications
A new approach for performing Particle Mesh Ewald in ab initio quantum
mechanical/molecular mechanical (QM/MM) simulations with extended atomic orbital basis …
mechanical/molecular mechanical (QM/MM) simulations with extended atomic orbital basis …