Methods

The Dynameomics project involves selecting protein domains for simulation to study both the native state (298 K) dynamics and the high temperature (498 K) unfolding behavior. The Target Selection page describes the criteria we use to select protein targets for simulation from our Consensus Domain Dictionary. We provide an overview of our simulation software in lucem molecular mechanics (ilmm) and our simulation protocols. Each native state simulation is then subjected to our quality control methods including comparison to NMR observables where possible, and methods to identify large structural rearrangements. Finally, we provide the details for our standard analysis suite run over all Dynameomics simulations. More advanced analysis can be found in Data Mining.