Computer-based molecular simulations are an important tool that is increasingly used to interpret experimental data and observations of biomolecular systems. Direct comparison between experiment and simulation is, however, seldom straightforward. Using examples from recent literature we have shown how computer simulation can complement experiment. Moreover, a critical analysis of various factors that may influence the degree of agreement between the results of simulations and experiments is presented.
COBISS.SI-ID: 29462021
The solvent structure and the conserved water sites with a specific orientation of water molecules with respect to the neighbouring helices of a three-stranded alpha-helical coiled coil have been determined using molecular dynamics simulations. The X-ray crystal structure of the coiled coil includes 21 possible water sites; however, the distinction between conserved water sites and water molecules, which are trapped at the specific positions due to crystal packing effects, is beyond crystallographic resolution.
COBISS.SI-ID: 30052613
In this paper we present the development of the molecular dynamics simulation technique and its use (i) to interpret experimental data (calculation of enthalpic and entropic components to Gibbs free energy that are experimentally difficult to access), ii) to provoke new experiments (calculation of ensembles of molecular configurations that can be compared to experimentally determined structures), iii) to replace experiments (experiments can be too difficult or too expensive to perform) and iv) to protect intellectual property.
COBISS.SI-ID: 29229829