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PDBrestore: A Free Web Interface for Processing and Fixing Protein Chains From Raw PDB Files.

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Bibliographic Details
Title: PDBrestore: A Free Web Interface for Processing and Fixing Protein Chains From Raw PDB Files.
Authors: Procacci, Piero1 (AUTHOR) piero.procacci@unifi.it
Source: Journal of Computational Chemistry. 5/15/2025, Vol. 46 Issue 13, p1-10. 10p.
Subjects: Drug design, Protein structure, Hydrogen atom, Bioinformatics software, Computational chemistry, Open source software, Tertiary structure
Abstract: We present PDBrestore, a free web interface for repairing protein PDB chains extracted from either a local PDB file or a PDB file downloaded from the Protein Data Bank. PDBrestore performs several key tasks: It adds hydrogen atoms, completes missing atoms in side chains, fills gaps in the sequence, derives the itp parameter file for a ligand according to the GAFF2 force field for GROMACS applications, and generates a reasonably pre‐equilibrated solvated simulation box. The interface is designed to streamline the cumbersome preparatory work required to set up an initial protein‐ligand coordinates PDB file for use in drug design projects, such as free energy perturbation or thermodynamic integration calculations of ligand binding affinities. Additionally, PDBrestore is available as a command‐line application within the open‐source ORAC distribution, which can be freely downloaded from the website: www1.chim.unifi.it/orac. [ABSTRACT FROM AUTHOR]
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Database: Engineering Source
Description
Abstract:We present PDBrestore, a free web interface for repairing protein PDB chains extracted from either a local PDB file or a PDB file downloaded from the Protein Data Bank. PDBrestore performs several key tasks: It adds hydrogen atoms, completes missing atoms in side chains, fills gaps in the sequence, derives the itp parameter file for a ligand according to the GAFF2 force field for GROMACS applications, and generates a reasonably pre‐equilibrated solvated simulation box. The interface is designed to streamline the cumbersome preparatory work required to set up an initial protein‐ligand coordinates PDB file for use in drug design projects, such as free energy perturbation or thermodynamic integration calculations of ligand binding affinities. Additionally, PDBrestore is available as a command‐line application within the open‐source ORAC distribution, which can be freely downloaded from the website: www1.chim.unifi.it/orac. [ABSTRACT FROM AUTHOR]
ISSN:01928651
DOI:10.1002/jcc.70124