ValidatorDB:Database contents

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For each validated motif, a validation report contains several types of results. Since the evaluation of the validated motif relies on comparing all atoms and bonds in the validated motif to those in the model residue, the first results that can be encountered are errors. In the first level Complete and Incomplete structures are distinguished. If you are unsure about the Terminology used in this section, please see this webpage.

Incomplete structures

Incomplete structures are validated residues, which were lacking atoms in their structure in comparison to the model residue, or the inter-atomic distances were way too big or too low. Namely:

  • Missing atoms: An atom in the model residue has no corresponding atom in the validated motif.
  • Missing rings: At least one missing atom originates from cycles (rings).
  • Degenerate: Those motifs could not be properly analyzed due their degenerate structure, i.e. suspicious discrepancies between the atoms and inter-atomic bonds in the validated motif and in the model residue prevented proper validation.

Please note, chirality is only evaluated for those motifs which are complete. This is because the absence of some atoms can prevent the proper evaluation of chirality on the chiral centers present in the validated motif. Therefore, note that all motifs which are counted in the Wrong chirality category are in fact complete. At the same time, the motifs with no missing atoms and no chirality error are actually counted in a category called Correct chirality.

ValidatorDB reports correct structures, as well as all potential issues found during validation, namely structures that are wrong either because they are incomplete (missing atoms or rings), or because the chirality of some atoms is incorrect. Here all the are potential issues of the incomplete structure are illustrated.

Complete structures

Complete structures can contain chirality issues on a variety of different atom types, here all possible cases occuring in ValidatorDB are illustrated.

Complete validated structures include all the atoms which are present in the model residue. However, there are still possible issues and warnings can be raised:

  • Wrong chirality: an atom from the validated motif has different chirality than the corresponding atom from the model residue. This category can be further specified by identifying a source of the chirality issue.
    • C atom: the chirality error was found on a single bonded carbon atom.
    • Planar atom: the chirality error was found on a planar chiral center. Because of their spacial distribution, planar chiral centers are very sensitive even to small perturbations in the position of the substituents. Therefore, some of the errors reported here might not be significant.
    • Metal atom: the chirality error was found on a metal chiral center.
    • High order atom: the chirality error was detected on an atom, which is bonded with a bond of higher order than one. A typical example is phosphorus.
    • Other: Additional chirality issue which could not be asserted to any of the above categories, for example chirality issues on Nitrogen.

Note that in case a validated residues belongs to more than one category, it can be found in all of them (i.e. Planar and Metal, which is often case of HEM residues)

  • Uncertain chirality: the presence of unusual bonds may cause an improper evaluation of chirality.
  • Substitution: An atom from the validated motif is of a different chemical element than the corresponding atom in the model residue (e.g. O mapped to N). This happens often at linkage sites.
  • Different naming: An atom from the validated motif has a different PDB atom name than the corresponding atom from the model residue (e.g. the C1 atom mapped to the C7 atom). This happens often when the original PDB files were produced by different software.
  • Foreign atom: An atom from the model residue was mapped to an atom from outside the validated residue (i.e. from its surroundings).
  • Alternate conformations: In the original PDB file, the validated residue contains atoms which were given in conformations (i.e., most probably different rotamers). Only the first rotamer was considered during validation.
  • Zero model RMSD: The superimposition between the model residue and the validated motif has a root mean square deviation of zero, i.e., the validated motif is identical to the model residue used as reference.

The last category Correct chirality includes all the validated residues, where all the atoms from the validated motif have a matching partner in the model structure and the chirality of the chiral atoms is correct. Last but not least, additional category Correct (Tolerant) chirality further includes motifs with identified chirality issues as Planar and High order since these might not be significant.

Furthermore, for each validation run, there is Processing warnings tab available, where one can find warnings about the processed structures. Typically, there is an information about skipped alternate conformation residues, wrong CONNECT records from the parent PDB file, processed models (in case the parent PDB is composed of multiple models) etc. Finally, as a general rule, in the validation interface, errors are marked in red (missing atoms) or dark yellow (wrong chirality), correct structures in green, and warnings in cyan.

ValidatorDB also reports warnings in the complete structures such as substitutions, different naming or foreign atoms.