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ValidatorDB
First Time User Guide

PDB-wide validation statistics: reports about
incomplete structures, incorrect chirality and
chemical modifications.
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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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Details by Molecule: Table summarizing validation results
for individual ligands and non-standard residues
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Hover the mouse over the name of a category to see its description.
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Sort the table according to the results from the selected category.

Add columns with additional categories of results.
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See results in percent's.
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Filter residues.
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See validation results for a selected residue.
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Molecule - MAN, Overview: Statistics of validation
results for all MAN ligands in the PDB
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See summary of results.
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Molecule - MAN, Summary: Statistics of validation
results for all MAN molecules in the PDB
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See detailed results.
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Molecule - MAN, Details: Detailed validation results
for all MAN molecules in the PDB
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Select a subset of results.
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See results for a single instance of the residue.
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1E4M_16_4280 (MAN): Details about an individual
molecule
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molecule
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Select the visualization mode you prefer

molecule
See superimposition of the validated and model molecule.
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See validation results for all ligands and non-standard residues in each
PDB entry. 21

Details by PDB Entry: Table summarizing validation
results for individual PDB entries
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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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See validation results for a selected PDB Entry.
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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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If you are looking for a specific molecule or a PDB entry you might want to try Search.
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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.

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

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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.

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ValidatorDB: First Time User Guide

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ValidatorDB: First Time User Guide