molclaw-pulchura-rebuild

Rebuild missing atoms in protein PDB structures for docking and simulation preparation.

28|2|Updated Mar 31, 2026

Search Tags:#simulation #bioinformatics #pdb #docking #pulchra #protein-reconstruction #structure-preparation

Ready to run

npx skills add https://github.com/InternScience/MolClaw --skill molclaw-pulchura-rebuild

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: molclaw-pulchura-rebuild
Source: https://github.com/InternScience/MolClaw/tree/main/skills/L1_tools/molclaw-pulchura-rebuild
Command: npx skills add https://github.com/InternScience/MolClaw --skill molclaw-pulchura-rebuild

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Reconstructs missing atoms and rebuilds incomplete protein PDB structures to enable reliable docking, virtual screening, and molecular dynamics preparation when experimental or modeled PDBs are truncated or missing sidechains and hydrogens.

Core Features & Use Cases

Mode-flexible rebuilding: Supports full, backbone-only, sidechain-only, and hydrogen-only reconstruction modes to match downstream workflow needs.
Per-file validation and reporting: Validates inputs, reports requested vs succeeded vs failed counts, and returns rebuilt PDB file paths and per-input error messages for troubleshooting.
Integration guidance: Advises preprocessing with PDB-fixing tools and requires explicit download of generated structure files to ensure reproducibility; ideal for preparing targets for docking or MD simulations.

Quick Start

Rebuild the uploaded PDB file my_protein.pdb in full mode with hydrogen-bond optimization enabled and then download all generated output structure files to local storage.

Frequently Asked Questions about molclaw-pulchura-rebuild

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I rebuild missing atoms in a PDB file for docking preparation?▼

To rebuild missing atoms in a PDB file for docking preparation, upload your structure and select a reconstruction mode like full, backbone, sidechain, or hydrogen. The tool validates inputs and returns rebuilt PDB files with per-input error reports.

What is the best way to prepare incomplete protein structures for molecular dynamics simulations?▼

Preparing incomplete protein structures for molecular dynamics requires reconstructing missing backbone, sidechain, or hydrogen atoms. You can apply full or partial reconstruction modes to truncated PDBs, then download the generated output files to ensure reproducibility in your simulation setup.

Can I batch process multiple PDB files for sidechain and hydrogen reconstruction?▼

Yes, you can batch process multiple PDB files for sidechain and hydrogen reconstruction. The tool supports batch PDB inputs, validates each file, and reports per-file success and failure counts alongside the specific error messages for any failed inputs.

Does PULCHRA support hydrogen-only reconstruction for virtual screening targets?▼

PULCHRA supports hydrogen-only reconstruction for virtual screening targets through its dedicated hydrogen mode. You can apply this to single or batch PDB inputs, allowing you to add missing hydrogen atoms while leaving existing backbone and sidechain structures intact.

Why do I need to download generated structure files after rebuilding my protein PDB?▼

You need to download generated structure files after rebuilding your protein PDB because the workflow mandates explicit local storage for reproducibility. Downloading the rebuilt PDB files ensures you retain the validated structures required for reliable downstream docking and simulation analysis.

When should I use full reconstruction instead of backbone-only mode for PDB structure preparation?▼

Use full reconstruction instead of backbone-only mode for PDB structure preparation when your target lacks both sidechain and hydrogen atoms. Full mode rebuilds all missing components, whereas backbone-only mode is suited for structures requiring just main chain atom repair before simulation.