The document provides a comprehensive user guide for ValidatorDB, detailing PDB-wide validation statistics related to incomplete structures, incorrect chirality, and chemical modifications. It includes tables summarizing validation results for individual ligands and non-standard residues, allowing users to sort, filter, and visualize the data. Additionally, it offers instructions on searching for specific entries or molecules and presents examples of validation errors commonly encountered.

1. ValidatorDB
First Time User Guide

2. PDB-wide validation statistics: reports about
incomplete structures, incorrect chirality and
chemical modifications.
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3. PDB-wide validation statistics: reports about
incomplete structures, incorrect chirality and
chemical modifications.
Would you like to see more details about validated molecules?
Click here.
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4. Details by Molecule: Table summarizing validation results
for individual ligands and non-standard residues
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5. Details by Molecule: Table summarizing validation results
for individual ligands and non-standard residues
Hover the mouse over the name of a category to see its description.
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Details by Molecule: Table summarizing validation results
for individual ligands and non-standard residues
Sort the table according to the results from the selected category.

7. Details by Molecule: Table summarizing validation results
for individual ligands and non-standard residues
Add columns with additional categories of results.
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8. Details by Molecule: Table summarizing validation results
for individual ligands and non-standard residues
See results in percent's.
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9. Details by Molecule: Table summarizing validation results
for individual ligands and non-standard residues
Filter residues.
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10. Details by Molecule: Table summarizing validation results
for individual ligands and non-standard residues
See validation results for a selected residue.
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11. Molecule - MAN, Overview: Statistics of validation
results for all MAN ligands in the PDB
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12. Molecule - MAN, Overview: Statistics of validation
results for all MAN ligands in the PDB
See summary of results.
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13. Molecule - MAN, Summary: Statistics of validation
results for all MAN molecules in the PDB
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14. Molecule - MAN, Overview: Statistics of validation
results for all MAN ligands in the PDB
See detailed results.
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15. Molecule - MAN, Details: Detailed validation results
for all MAN molecules in the PDB
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16. Molecule - MAN, Details: Detailed validation results
for all MAN molecules in the PDB
Select a subset of results.
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17. Molecule - MAN, Details: Detailed validation results
for all MAN molecules in the PDB
See results for a single instance of the residue.
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18. 1E4M_16_4280 (MAN): Details about an individual
molecule
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19. 1E4M_16_4280 (MAN): Details about an individual
molecule
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Select the visualization mode you prefer

20. 1E4M_16_4280 (MAN): Details about an individual
molecule
See superimposition of the validated and model molecule.
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21. Details by Molecule: Table summarizing validation results
for individual ligands and non-standard residues
See validation results for all ligands and non-standard residues in each
PDB entry. 21

22. Details by PDB Entry: Table summarizing validation
results for individual PDB entries
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23. Details by PDB Entry: Table summarizing validation
results for individual PDB entries
The table “Details by PDB Entry” can be operated with the same as the table
“Details by Molecule”, i.e.: Sort according to the results of different categories, add
columns with categories, see results in %.
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24. Details by PDB Entry: Table summarizing validation
results for individual PDB entries
See validation results for a selected PDB Entry.
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25. PDB Entry – 3D12: Statistics of validation results for
PDB entry 3D12
The validation results for the ligands and non-standard residues in PDB entry
3D12 are organized in a similar manner as for the previously discussed MAN
molecule: summary of the validation report and detailed results.
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26. Details by PDB Entry: Table summarizing validation
results for individual PDB entries
If you are looking for a specific molecule or a PDB entry you might want to try Search.
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27. 27
Search: Select criterion for obtaining a validation
report of specific entries or molecules

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Search: Select criterion for obtaining a validation
report of specific entries or molecules
See examples of molecules and PDB entries, which exhibit errors either very
commonly or very rarely. Detailed instructions about using the Search are also
available.

29. 29
Samples: Examples of molecules and PDB entries,
which exhibit errors either very commonly or very
rarely.

30. 30
Samples: Examples of molecules and PDB entries,
which exhibit errors either very commonly or very
rarely.
See Step-by-step tutorials on how to use the ValidatorDB search functions.