Editing ValidatorDB:Database contents (section)

=Warnings=
[[File:VDB warnings.png|thumb|right|700px| Examples of ''warnings'' reported during the ''advanced'' analyses.]]

Aside from the ''completeness'' and ''chirality'' analyses, '''ValidatorDB''' and '''MotiveValidator''' also perform a set of ''advanced'' analyses. These are meant to bring attention to aspects which may be indicators of further problems in the structure, or, on the contrary, explain why some errors were found during the ''completeness'' and ''chirality'' analyses. For example, if a molecule is part of a polymer, a reported change in chirality might be a consequence of some glitch in the polymer building process. Of course, each situation should be studied individually, but the ''advanced'' analyses provide a good starting point.

When issues are found during an ''advanced'' analysis, a warning is reported: 
* '''Substitution''': An atom from the validated molecule is of a different chemical element than the corresponding atom in the model (e.g. O from the model is mapped to N from the validated molecule). This happens often at linkage sites for ligands which are covalently bound to biomolecules.
* '''Different naming''': An atom from the validated molecule has a different PDB atom name than the corresponding atom from the model (e.g. the C1 atom from the model is mapped to the C7 atom from the validated molecule). This happens often when the original PDB files were produced by different software.
* '''Foreign atom''': An atom from the model was mapped to an atom from outside the validated molecule (i.e. from its surroundings). This happens often at linkage sites for polymeric ligands or ligands which are covalently bound to biomolecules.
* '''Alternate conformations''': In the original PDB file, the validated molecule contains at least some parts (some or all atoms) for which alternate conformers were given (i.e., most probably different rotamers). Only the first conformer was considered during validation.
* '''Zero model RMSD''': The superimposition between the model and the validated molecule has a root mean square deviation of zero, i.e., the validated molecule is identical to the model used as reference.

While the results of the ''Advanced'' analyses have no bearing over the chemical soundness of the validated molecules, they indicate that further, especially automated processing of these structures can be very problematic. Comparison between the structures of molecules with the same annotation (3-letter code) from different PDB entries might even be impossible in the presence of a substitution, as the corresponding atoms have different chemical elements. PDB atom names cannot be used straightforwardly, since even element symbols can differ and atoms can be formally included in neighboring residues.

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