Alternative sidechain conformations in the interface are not allowed.
- Hydrogens are not required and are not considered.
- Peptide ligands can be scanned if they only contain standard amino acids. For this purpose, ligand entries in the PDB file have to be modified: Please change HETATM to ATOM entries and define a chain identifier of your choice.
- Make sure that you select the right chain(s). Select only the chains that should be mutated.
Important: If you want to perform alanine scanning for both of two oppositely arranged polypeptide chains, you have to scan each of the chains SEPARATELY.
- Make sure that you select all chains from the protein of your interest. Otherwise, calculation of INTRAmolecular interactions can lead to false predictions.
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