The SolvX Server
Structure Validation - Solvation Preference
This server computes the solvation profile for a protein structure. This is useful when assessing the quality of
a homology model or an existing PDB structure used in homology modelling.
Solvation preference is a measure of solvent accessibility for each residue within a protein; a well-packed
structure should have an overall solvation preference below zero. Generally, the more negative this figure is,
the better the model. A solvation profile graph is returned for each chain/model, and the raw data are also
downloadable.
Notes
- This server takes as input the atomic coordinates of a protein structure. Your file need only contain ATOM/HETATM entries, although full PDB format files are fine.
- However, if your file contains more than one chain or structure, TER lines should be used to terminate and thereby separate each of these.
- If your structure file contains a large number of chains, you are advised to remove all but the first chain. Alternatively, use the «first chain only» option above.
- For each chain, a graph is returned displaying the solvation profile residue-by-residue, plus an averaged profile over a sliding window of size 11 residues. The total solvation preference for the structure is also returned.
Reference