ArticleJournal of computational chemistry2025
PDBrestore: A Free Web Interface for Processing and Fixing Protein Chains From Raw PDB Files.
Article in Journal of computational chemistry, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1 citing paper in PubMed.
- Unlocking the potential of marine natural product fragments for rational anticancer drug design: a computational approach.Scientific reports · 2026Article
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1 author.
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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.
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