The CABS-based procedure for the simulation of near-native dynamics has been made available as a CABS-flex web server (Jamroz et al., 2013a).
Following this work, we implemented the developed CABS-model-based protocol for fast simulations of near-native dynamics in a web server called CABS-flex (Jamroz et al., 2013a).
Importantly, the computational cost of obtaining near-native dynamics by CABS simulations was proved to be much lower (∼6 × 10 times) than that of MD [technically, this is the cost of achieving a residue fluctuation profile that best fits that obtained from 10 ns MD simulations, see details in Jamroz et al. (2013b)].
The CABS-flex method follows our earlier work (Jamroz et al., 2013b) where we demonstrated that the consensus view of protein near-native dynamics obtained from 10 ns MD simulations (all-atom, explicit water, using the four most popular force-fields for all protein metafolds) is consistent with dynamics from the CABS model.
On the other hand, because the functional landscape topographies are complicated, the native state dynamics are often difficult to interpret.
Overall, our results provide a more complete picture of the energy landscape of the native state dynamics of an AR domain.
Mimicking native functional dynamics for traditional biomaterials such as thermoset elastomers is limited due to their lack of responsiveness to biological stimuli and difficulties to incorporate biofunctionalities.
P. radiata plantations should be incorporated in the conservation scenario of the Maulino Forest plant species, introducing new procedures to reduce the impact of forest replacement on native plant dynamics.
This study provides useful information to improve rangeland management decisions as well as assessing native invasive dynamics with potential applications for assessing its effects on wildlife habitat, livestock operations, and habitat restoration strategies.
All the changes in the native state dynamics induced by the mutations reverberate as a reorganization of reactive regions, sites entailing the recognition of small molecules, antibodies or self-association events.
