Pdbe Validation Tools

Configuration File: pdbe_validation_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the pdbe_validation_tools.json configuration file.

Available Tools

PDBeValidation_get_outlier_residues (Type: PDBeValidationTool)

Get residue-level validation outliers for a PDB structure from PDBe. Identifies specific residues…

PDBeValidation_get_outlier_residues tool specification

Tool Information:

  • Name: PDBeValidation_get_outlier_residues

  • Type: PDBeValidationTool

  • Description: Get residue-level validation outliers for a PDB structure from PDBe. Identifies specific residues with geometry problems (Ramachandran outliers, sidechain rotamer outliers, bond angle/length deviations). Returns problematic residues organized by molecule/chain. Essential for identifying unreliable regions before using structure data for molecular docking, mutation analysis, or protein engineering. Example: 4HHB has residue-level outliers in chains A-D with rotamer and Ramachandran deviations.

Parameters:

  • pdb_id (string) (required) PDB identifier (4-character code). Case-insensitive. Examples: ‘4hhb’, ‘1tup’, ‘6lu7’.

Example Usage:

query = {
    "name": "PDBeValidation_get_outlier_residues",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)

PDBeValidation_get_quality_scores (Type: PDBeValidationTool)

Get global quality validation scores for a PDB structure from PDBe. Returns percentile rankings f…

PDBeValidation_get_quality_scores tool specification

Tool Information:

  • Name: PDBeValidation_get_quality_scores

  • Type: PDBeValidationTool

  • Description: Get global quality validation scores for a PDB structure from PDBe. Returns percentile rankings for Ramachandran outliers, rotamer outliers, and clashscore. Each metric has a raw value, an absolute percentile (compared to all structures), and a relative percentile (compared to structures at similar resolution). Higher percentile = better quality. Essential for assessing whether a structure is reliable enough for downstream analysis. Example: 4HHB (hemoglobin) has clashscore raw=141.11 (absolute: 0.0%, relative: 0.0% - very poor by modern standards); 1TUP (p53-DNA complex) has similar vintage quality issues.

Parameters:

  • pdb_id (string) (required) PDB identifier (4-character code). Case-insensitive. Examples: ‘4hhb’ (hemoglobin), ‘1tup’ (p53-DNA), ‘6lu7’ (SARS-CoV-2 main protease).

Example Usage:

query = {
    "name": "PDBeValidation_get_quality_scores",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)