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

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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]
Copyright of Journal of Computational Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
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PubType: Academic Journal
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  Data: PDBrestore: A Free Web Interface for Processing and Fixing Protein Chains From Raw PDB Files.
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  Data: <searchLink fieldCode="AR" term="%22Procacci%2C+Piero%22">Procacci, Piero</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> piero.procacci@unifi.it</i>
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  Data: <searchLink fieldCode="DE" term="%22Drug+design%22">Drug design</searchLink><br /><searchLink fieldCode="DE" term="%22Protein+structure%22">Protein structure</searchLink><br /><searchLink fieldCode="DE" term="%22Hydrogen+atom%22">Hydrogen atom</searchLink><br /><searchLink fieldCode="DE" term="%22Bioinformatics+software%22">Bioinformatics software</searchLink><br /><searchLink fieldCode="DE" term="%22Computational+chemistry%22">Computational chemistry</searchLink><br /><searchLink fieldCode="DE" term="%22Open+source+software%22">Open source software</searchLink><br /><searchLink fieldCode="DE" term="%22Tertiary+structure%22">Tertiary structure</searchLink>
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  Data: 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]
– Name: AbstractSuppliedCopyright
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  Data: <i>Copyright of Journal of Computational Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1002/jcc.70124
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      – Code: eng
        Text: English
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        PageCount: 10
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      – SubjectFull: Drug design
        Type: general
      – SubjectFull: Protein structure
        Type: general
      – SubjectFull: Hydrogen atom
        Type: general
      – SubjectFull: Bioinformatics software
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      – SubjectFull: Computational chemistry
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      – SubjectFull: Open source software
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      – SubjectFull: Tertiary structure
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      – TitleFull: PDBrestore: A Free Web Interface for Processing and Fixing Protein Chains From Raw PDB Files.
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              Text: 5/15/2025
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              Y: 2025
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            – TitleFull: Journal of Computational Chemistry
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