Features
In INPS3D, the set of INPS descriptors also includes features derived from protein 3D structure.
In particular, the following two additional structure-based descriptors are considered:
- one descriptor corresponding to the Relative Solvent Accessibility (RSA) of the native residue.
The absolute solvent accessibility is computed from the PDB file using the DSSP method (Kabsch and Sander, 1983) and then normalized as previously described in Rost and Sander (1994); - another descriptor encodes for the local energy difference (ED) between native and mutated protein structures.
Input
To start using INPS-3D you need to submit PDB and mutation files, insert the protein chain and press the "Submit job" button.
The server accepts a single PDB file.
Output
There are two main sections in the result page:
- Sequence view:
general information about the protein, including PDB ID and the protein length.
Residues that are involved in prediction are highlighted in blue in a sequence view panel. - Detailed mutation report:
On the top-left of the table, there is a button to download the results in a text format.
Below, there is the prediction of Stability change (DDG) in kcal/mol for each submitted mutation.