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ValidatorDB 
First Time User Guide
PDB-wide validation statistics: reports about 
incomplete structures, incorrect chirality and 
chemical modifications. 
2
PDB-wide validation statistics: reports about 
incomplete structures, incorrect chirality and 
chemical modifications. 
Wo...
Details by Molecule: Table summarizing validation results 
for individual ligands and non-standard residues 
4
Details by Molecule: Table summarizing validation results 
for individual ligands and non-standard residues 
Hover the mou...
6 
Details by Molecule: Table summarizing validation results 
for individual ligands and non-standard residues 
Sort the t...
Details by Molecule: Table summarizing validation results 
for individual ligands and non-standard residues 
Add columns w...
Details by Molecule: Table summarizing validation results 
for individual ligands and non-standard residues 
See results i...
Details by Molecule: Table summarizing validation results 
for individual ligands and non-standard residues 
Filter residu...
Details by Molecule: Table summarizing validation results 
for individual ligands and non-standard residues 
See validatio...
Molecule - MAN, Overview: Statistics of validation 
results for all MAN ligands in the PDB 
11
Molecule - MAN, Overview: Statistics of validation 
results for all MAN ligands in the PDB 
See summary of results. 
12
Molecule - MAN, Summary: Statistics of validation 
results for all MAN molecules in the PDB 
13
Molecule - MAN, Overview: Statistics of validation 
results for all MAN ligands in the PDB 
See detailed results. 
14
Molecule - MAN, Details: Detailed validation results 
for all MAN molecules in the PDB 
15
Molecule - MAN, Details: Detailed validation results 
for all MAN molecules in the PDB 
Select a subset of results. 
16
Molecule - MAN, Details: Detailed validation results 
for all MAN molecules in the PDB 
See results for a single instance ...
1E4M_16_4280 (MAN): Details about an individual 
molecule 
18
1E4M_16_4280 (MAN): Details about an individual 
molecule 
19 
Select the visualization mode you prefer
1E4M_16_4280 (MAN): Details about an individual 
molecule 
See superimposition of the validated and model molecule. 
20
Details by Molecule: Table summarizing validation results 
for individual ligands and non-standard residues 
See validatio...
Details by PDB Entry: Table summarizing validation 
results for individual PDB entries 
22
Details by PDB Entry: Table summarizing validation 
results for individual PDB entries 
The table “Details by PDB Entry” c...
Details by PDB Entry: Table summarizing validation 
results for individual PDB entries 
See validation results for a selec...
PDB Entry – 3D12: Statistics of validation results for 
PDB entry 3D12 
The validation results for the ligands and non-sta...
Details by PDB Entry: Table summarizing validation 
results for individual PDB entries 
If you are looking for a specific ...
27 
Search: Select criterion for obtaining a validation 
report of specific entries or molecules
28 
Search: Select criterion for obtaining a validation 
report of specific entries or molecules 
See examples of molecule...
29 
Samples: Examples of molecules and PDB entries, 
which exhibit errors either very commonly or very 
rarely.
30 
Samples: Examples of molecules and PDB entries, 
which exhibit errors either very commonly or very 
rarely. 
See Step-...
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ValidatorDB: First Time User Guide

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Walk through to the ValidatorDB (http://ncbr.muni.cz/ValidatorDB), a database of ligand validation results of Protein Data Bank.

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ValidatorDB: First Time User Guide

  1. 1. ValidatorDB First Time User Guide
  2. 2. PDB-wide validation statistics: reports about incomplete structures, incorrect chirality and chemical modifications. 2
  3. 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. 3
  4. 4. Details by Molecule: Table summarizing validation results for individual ligands and non-standard residues 4
  5. 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. 5
  6. 6. 6 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. 7. Details by Molecule: Table summarizing validation results for individual ligands and non-standard residues Add columns with additional categories of results. 7
  8. 8. Details by Molecule: Table summarizing validation results for individual ligands and non-standard residues See results in percent's. 8
  9. 9. Details by Molecule: Table summarizing validation results for individual ligands and non-standard residues Filter residues. 9
  10. 10. Details by Molecule: Table summarizing validation results for individual ligands and non-standard residues See validation results for a selected residue. 10
  11. 11. Molecule - MAN, Overview: Statistics of validation results for all MAN ligands in the PDB 11
  12. 12. Molecule - MAN, Overview: Statistics of validation results for all MAN ligands in the PDB See summary of results. 12
  13. 13. Molecule - MAN, Summary: Statistics of validation results for all MAN molecules in the PDB 13
  14. 14. Molecule - MAN, Overview: Statistics of validation results for all MAN ligands in the PDB See detailed results. 14
  15. 15. Molecule - MAN, Details: Detailed validation results for all MAN molecules in the PDB 15
  16. 16. Molecule - MAN, Details: Detailed validation results for all MAN molecules in the PDB Select a subset of results. 16
  17. 17. Molecule - MAN, Details: Detailed validation results for all MAN molecules in the PDB See results for a single instance of the residue. 17
  18. 18. 1E4M_16_4280 (MAN): Details about an individual molecule 18
  19. 19. 1E4M_16_4280 (MAN): Details about an individual molecule 19 Select the visualization mode you prefer
  20. 20. 1E4M_16_4280 (MAN): Details about an individual molecule See superimposition of the validated and model molecule. 20
  21. 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. 22. Details by PDB Entry: Table summarizing validation results for individual PDB entries 22
  23. 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 %. 23
  24. 24. Details by PDB Entry: Table summarizing validation results for individual PDB entries See validation results for a selected PDB Entry. 24
  25. 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. 25
  26. 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. 26
  27. 27. 27 Search: Select criterion for obtaining a validation report of specific entries or molecules
  28. 28. 28 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. 29 Samples: Examples of molecules and PDB entries, which exhibit errors either very commonly or very rarely.
  30. 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.
  • BlayneWenzel

    Aug. 10, 2018

Walk through to the ValidatorDB (http://ncbr.muni.cz/ValidatorDB), a database of ligand validation results of Protein Data Bank.

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