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 …
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models
PA Kollman, I Massova, C Reyes, B Kuhn… - Accounts of chemical …, 2000 - ACS Publications
A historical perspective on the application of molecular dynamics (MD) to biological
macromolecules is presented. Recent developments combining state-of-the-art force fields …
macromolecules is presented. Recent developments combining state-of-the-art force fields …
Theory and applications of the generalized Born solvation model in macromolecular simulations
V Tsui, DA Case - Biopolymers: Original Research on …, 2000 - Wiley Online Library
Generalized Born (GB) models provide an attractive way to include some thermodynamic
aspects of aqueous solvation into simulations that do not explicitly model the solvent …
aspects of aqueous solvation into simulations that do not explicitly model the solvent …
Approaches to the description and prediction of the binding affinity of small‐molecule ligands to macromolecular receptors
The influence of a xenobiotic compound on an organism is usually summarized by the
expression biological activity. If a controlled, therapeutically relevant, and regulatory action …
expression biological activity. If a controlled, therapeutically relevant, and regulatory action …
New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations
The accurate simulation of DNA and RNA has been a goal of theoretical biophysicists for a
number of years. That is, given a high-resolution experimental structure, or perhaps a …
number of years. That is, given a high-resolution experimental structure, or perhaps a …
All‐atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
Molecular dynamics simulations based on empirical force fields can greatly enhance
knowledge of DNA and RNA structure and dynamics in solution. Presented are results on …
knowledge of DNA and RNA structure and dynamics in solution. Presented are results on …
Theoretical methods for the description of the solvent effect in biomolecular systems
The environment plays a key role in the determination of the properties and reactivity of
substances in condensed phases. The complexity of chemical phenomena in solution has …
substances in condensed phases. The complexity of chemical phenomena in solution has …
Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects
J Srinivasan, MW Trevathan, P Beroza… - Theoretical Chemistry …, 1999 - Springer
The Poisson–Boltzmann (PB) continuum solvent model shows considerable promise in
providing a description of electrostatic solvation effects in biomolecules, but it can be …
providing a description of electrostatic solvation effects in biomolecules, but it can be …
Molecular dynamics simulations of nucleic acids with a generalized Born solvation model
V Tsui, DA Case - Journal of the American Chemical Society, 2000 - ACS Publications
A generalized Born (GB) model has been applied to molecular dynamics simulations of the
A-and B-forms of a duplex DNA d (CCAACGTTGG) 2 and the corresponding duplex RNA r …
A-and B-forms of a duplex DNA d (CCAACGTTGG) 2 and the corresponding duplex RNA r …
Molecular dynamics simulation of nucleic acids: successes, limitations, and promise
In the last five years we have witnessed a significant increase in the number publications
describing accurate and reliable all‐atom molecular dynamics simulations of nucleic acids …
describing accurate and reliable all‐atom molecular dynamics simulations of nucleic acids …