What can I do with the DrugScorePPI web server?
Please read the welcome page again.
What do I need to perform an alanine-scanning?
You need a PDB file (*.pdb) or the PDB code. Please note that alternative sidechain conformations are not allowed in the interface. Furthermore, you need to know the chain identifier of the chain where an alanine scanning should be performed. The identifier must be exactly the same as in the PDB file.
How can I perform an alanine-scanning on multiple chains?
Provide all chains you are interested in as a comma-separated list (e.g., A,B). All chains must be from one binding partner.
What about the chains corresponding to the chain I want to mutate?
DrugScorePPI will automatically detect the interface by selecting every residue in any corresponding chain within 5 Angstrom distance from the chosen chain(s).
What is the 'Degree of Buriedness'?
The degree of buriedness describes the sidechains' surrounding by considering the number of atoms of nearby residues within a radius of 4 Angstrom. The higher the value, the more buried is a sidechain.
What is meant by 'Possible Saltbridges' ?
Saltbridges in protein interfaces are always a hint to a possible hotspot. Therefore, this feature detects possible residue pairs that can be involved in a saltbridge, e.g., ASP or GLU and ARG. If a sidechain is found within 4 Angstrom radius from the mutated residue that could be able to form a saltbridge, the mutated residue is marked by an 'X'.
Is there any error estimate?
Yes, the standard deviation between computed and experimental ΔΔG values is 0.9 kcal/mol for a leave-one-out crossvalidation on 309 Ala mutants and 1.11 kcal/mol for an external test set of 22 Ala mutants. The mean experimental error reported for 78 of the 309 Ala mutants is 0.31 kcal/mol.
What do the warning messages mean?
There are two types of warning messages: (1) Missing residues and/or atoms in protein-protein interfaces can have a large impact on computed ΔΔG values. For that reason, if declared in the PDB header, a warning message is issued residues and/or atoms are missing in the protein complex of interest. (2) Providing valid chain identifiers is crucial. E.g., if alanine scanning on chain 'A' of binding partner I of a complex is requested, but protein I consists of chains A and B, intramolecular interactions between A and B will be falsely considered in the ΔΔG values. Thus, if appropriate information is available in the PDB header,a warning will be issued that protein I consists of chains 'A B' and not only of chain 'A'. When uploading a PDB file of your own, please note that such a warning can only be shown if a valid PDB header is available in your file.
I got a logfile as result. Where is the problem?
Most errors during alanine-scanning occur because of wrong input data. Please have a look at the ERROR message at the end of the logfile. If this does not help you, please contact the support.
What can not be done with the DrugScorePPI web server?
DrugScorePPI cannot predict changes in the binding free energy that depend on INTRAmolecular interactions. Hence, contributions to the binding free energy that originate from conformational changes and/or unfolding-folding transitions of one binding partner are not captured.