The AllosMod-FoXS server is a combination of FoXS and
AllosMod. AllosMod is a server to sample protein conformations, which
was originally created to study allosteric proteins. FoXS is a server to do rigid body modeling of small angle X-ray scattering (SAXS)
profiles. The combined server is meant to create a user friendly way to generate structures to compare to experimental SAXS profiles.
The structures that are generated are a result of an underlying energy landscape and sampling procedure. The energy landscapes are constructed with the assumption/hypothesis that the most stable structure for a given sequence is the native crystal structure. In some instances, there might be several stable structures, in which case the energy landscape should include multiple basins of attraction. AllosMod is a tool that allows the user to specify what structures should define the energy landscape. Crystal structures or models of protein, DNA, RNA, and sugars may be used.
There are different sampling options listed from least diverse sampling to most diverse sampling. As you go down the list, sampled structures will increasingly deviate from the inputted PDB files:
These default settings can be adjusted with more flexibility by using AllosMod, which
allows the user to download the scripts and log files. These scripts can be ran on the user's computer using MODELLER. For help,
click here. With AllosMod, you will also be able to generate
models based on a thermodynamically well sampled energy landscape. If this energy landscape produces models that reproduce
SAXS data, then perhaps the user can learn how the microscopic motions are relevant to the biological function of the protein.