The influence of flexible walls on the self-diffusion of CH4 in an isolated single walled carbon nanotube, as an example, is studied by molecular dynamics simulations. By simulating the carbon nanotube as a flexible framework we demonstrate that the flexibility has a crucial influence on self-diffusion at low loadings. We show how this influence can be incorporated in a simulation of a rigid na...

A nucleotide-by-nucleotide density fitting procedure has been successfully developed and has been applied to an analysis of a domain of the Tetrahymena ribozyme and a TBP-DNA interaction. This procedure is described in a paper that has been submitted for publication [Pastor, N., Weinstein, H., Jamison, E. & Brenowitz, M. A Detailed Interpretation of OH Radical Footprints in a TBP-DNA Complex Re...

Fitting of atomic components into electron cryo-microscopy (cryoEM) density maps is routinely used to understand the structure and function of macromolecular machines. Many fitting methods have been developed, but a standard protocol for successful fitting and assessment of fitted models has yet to be agreed upon among the experts in the field. Here, we created and tested a protocol that highli...

0022-2836/$ see front matter q 2005 E Present address: S. Falke, Departm William Jewell College, 500 College 64068, USA. Abbreviations used: EM, electron single large monomer of glutamine normal mode flexible fitting. E-mail addresses of the correspon [email protected]; mfisher1@kumc The 13 Å resolution structures of GroEL bound to a single monomer of the protein substrate glutamine synthetase (G...

Few methods use molecular dynamics simulations in concert with atomically detailed force fields to perform protein–ligand docking calculations because they are considered too time demanding, despite their accuracy. In this paper we present a docking algorithm based on molecular dynamics which has a highly flexible computational granularity. We compare the accuracy and the time required with wel...

Few methods use molecular dynamics simulations based on atomically detailed force fields to study the proteinligand docking process because they are considered too time demanding despite their accuracy. In this paper we present a docking algorithm based on molecular dynamics simulations which has a highly flexible computational granularity. We compare the accuracy and the time required with wel...