UltraScan - SOMO (SOlution MOdeller) Workshop
The focus of this workshop will be on how to compute the hydrodynamic parameters, that can be measured experimentally, starting from high or medium resolution structures (PDB files or dummy atoms models from SAXS/SANS experiments). The theory behind the bead modeling methods will be BRIEFLY exposed, but the main focus will be on a guided tour of the new implementation of SOMO within the UltraScan (US) suite (Brookes et al., Eur. J. Biophys 2009, in press).
Partial list of topics:
- Handling of PDB files, including dealing with missing atoms/residues
- Accessible surface area (ASA) computation to discriminate buried from exposed residues, and re-check of the final bead model
- Rules for converting groups of atoms into beads and appropiately positioning them, as implemented in user-editable files, and how to deal with "new" (=not-yet-coded) residues
- Overlap removal
- Structures and models visualization using RasMol
- Hydrodynamic computations
- Further reduction of the number of beads for large structures and for dummy-atoms models by the use grid-based functions (AtoB).
Test proteins will be used as an example, but attendees are encouraged to bring their own structures to be modeled "live".
More information about US-SOMO can be found in the UltraScan-SOMO manual pages.
Instructor: Mattia Rocco, IST, Genova, Italy