ValidatorDB:UserManual

ValidatorDB is a database of precomputed validation results for all ligands and non-standard residues in the Protein Data Bank (PDB). The molecules deemed relevant for validation are all ligands and non-standard residues with 7 or more heavy atoms. Standard nucleotides, standard amino acids and selenomethionine are not covered. The models from the wwPDB Chemical Component Dictionary (wwPDB CCD) are used as reference structures during validation. The database is updated on a weekly basis.

Below you can find all the information you need in order to make efficient use of ValidatorDB.

First time user guide to ValidatorDB

If you are a first time user, we recommend that you go through the basic presentation specifically prepared to help you get oriented.

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Terminology

• Residue
• Non-standard residue
• Ligand
• Molecule
• Model
• Input motif

Principles

• Validation procedure
• Validation analyses
• Validation results
• Validation reports

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Database contents

1. Incomplete structures
2. Complete structures
   1. Wrong chirality
   2. Correct chirality
3. Warnings
4. Processing warnings

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Database organization

1. Synopsis page
   1. Overview
   2. Details by molecule
   3. Details by PDB entry
   4. Custom search
2. Specifics page
   1. Overview
   2. Summary
   3. Details
   4. Single molecule report
   5. Processing warnings

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