David A. Case

TL;DR: The most recent developments, since version 9 was released in April 2006, of the Amber and AmberTools MD software packages are outlined, referred to here as simply the Amber package.

TL;DR: This paper applied continuum solvent models to investigate the relative stability of A-and B-form helices for three DNA sequences, d(CCAACGTTGG), d(ACCCGCGGGT), and d(CGCGAATTCGCG)2, a phosphoramidate-mod...

TL;DR: This study investigates the capability of the molecular mechanics-generalized Born surface area (GBSA) approach to estimate absolute binding free energies for the protein-protein complexes and finds hotspot residues experience a significantly larger-than-average decrease in local fluctuations upon complex formation.

TL;DR: An overview of one such approximation, the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids, and focuses particularly on versions of the generalized born model that have a pair-wise analytical form, and therefore fit most naturally into conventional molecular mechanics calculations.

TL;DR: The analytic generalized Born approximation is modified to permit a more accurate description of large macromolecules, while its established performance on small compounds is nearly unaffected, and is adapted to describe molecules with an interior dielectric constant not equal to unity.