Ruud M. Scheek

TL;DR: This procedure combines model building with a restrained molecular dynamics algorithm, in which distance information from nuclear Overhauser effects is incorporated in the form of pseudo potentials, to determine the three-dimensional structure of biomolecules from nuclear magnetic resonance data.

TL;DR: The molecular dynamics simulations show that the time-averaged constraints increase the mobility allowed to molecules, produce better agreement with distance bounds, improve searching properties and give a better estimate of the conformational space occupied by the molecule in solution.

TL;DR: Applications to an IgG‐binding domain, an SH3 binding domain, HPr, calmodulin, and lysozyme are presented which illustrate the use of the method as a fast and simple way to predict structural variability in proteins.

TL;DR: In this article, a method for enforcing nuclear Overhauser effect (NOE) distance restraints in molecular dynamics simulations is presented, in which a term is included in the force field such that the distance restraint need only be satisfied as a ǫ r −3 −1/3 weighted time average over the simulation trajectory.

TL;DR: A sequential assignment procedure is outlined, based on two-dimensional NOE and J-correlated spectroscopy, for assigning the nonexchangeable proton resonances in NMR spectra of oligonucleotides of intermediate size.