Repair protein PDB files by fixing missing atoms and residues.
npx skills add https://github.com/InternScience/MolClaw --skill molclaw-pdbfixer
Please help me install this Agent Skill. Skill: molclaw-pdbfixer Source: https://github.com/InternScience/MolClaw/tree/main/skills/L1_tools/molclaw-pdbfixer Command: npx skills add https://github.com/InternScience/MolClaw --skill molclaw-pdbfixer
This Skill automates repair and standardization of protein PDB structure files to fix missing atoms and residues, add hydrogens at a specified pH, remove heterogens or waters, and replace nonstandard residues to produce validated files for downstream modeling.
Use molclaw-pdbfixer to repair 'input.pdb', add hydrogens at pH 7.0, remove heterogens, and download the repaired PDB to the local workspace.
High-intent search queries and answers about installing and using this skill.
To repair missing atoms in a PDB file, use a structure preparation tool to fill incomplete residues, model missing segments, and add hydrogens. This produces a validated PDB file with complete topology for downstream docking or simulation workflows.
Adding hydrogens to a protein structure at a specific pH involves applying a protonation algorithm that adjusts hydrogen placement based on the target pH environment. This standardizes the PDB file by ensuring correct ionization states for molecular dynamics simulations.
Yes, batch preprocessing workflows support cleaning multiple PDB files by removing heterogens and water molecules. This generates sanitized protein structures with reported atom, residue, and chain counts for each processed file.
Yes, verifying repaired PDB structures requires downloading the output file to your local workspace to confirm the updated atom, residue, and chain counts. A dry-run validation mode is also available to check structural integrity without writing the final file.
Replacing nonstandard residues before molecular dynamics simulations ensures the PDB file contains only recognized amino acid types for accurate force field parameterization. This standardization prevents topology generation errors and ensures simulation stability.
yf8578Query the RCSB PDB database for protein structures by text, gene name, or method.
InternSciencePerforms GPU-accelerated molecular docking and generates pose files with affinity values.
InternScienceRepair and clean PDB files with PDBFixer and output topology counts.
JosephWoodallSearch and fetch 3D structural data from the RCSB PDB repository.
