Stefan Boresch

TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.

TL;DR: A versatile set of restraints is described that can be used in MD simulations, that restricts both the position and the orientation of the ligand, and that is defined relative to the receptor rather than relative to a fixed point in space.

TL;DR: In this commentary, difficulties with comparative modeling at low sequence identity are discussed, the degree of structural conservation to be expected within the superfamily is analyzed and numerical estimates of model uncertainties in functional regions are provided.

TL;DR: Comparative models of the extracellular and transmembrane domains of GABAA receptors in the agonist-free state based on the recently published structures of the nicotinic acetylcholine receptor were generated and can now be used to design new experiments for clarification of pharmacological and structural questions as well as for investigating and visualizing drug induced conformational changes.

TL;DR: It is shown that a linear coupling scheme for the alchemical creation of a chemical identity corresponds to a particularly useful path because it leads to a symmetric decoupling of the free energy components.