PDB-Tools Web

PDB-Tools Web provides manipulation and processing of Protein Data Bank (PDB) files for structural biology tasks such as validation, modification, and preparation for computational modeling.

Key Features:

• Extensive toolkit: Integrates over 40 individual utilities from the pdb-tools suite for diverse PDB file manipulations.
• Pipeline composition: Enables chaining multiple pdb-tools utilities into sequential pipelines for reproducible file processing.
• PDB-format-aware operations: Includes functions that address common PDB-format inconsistencies and perform file-level edits and transformations.

Scientific Applications:

• Structure validation: Assists in checking and correcting PDB-format and macromolecular structure issues prior to analysis.
• Structure modification: Supports editing and transformation of PDB files for downstream analyses.
• Preparation for computational modeling: Prepares and standardizes PDB files for input into modeling and simulation workflows.

Methodology:

Integration of the pdb-tools suite (over 40 command-line utilities) and composition of those utilities into sequential pipelines to perform PDB file transformations.