Guide · Target preparation
Protein cleaning
Import a raw PDB structure, remove unwanted components, add hydrogens, and produce a modeling-ready receptor.
Prerequisites
A raw PDB file or PDB accession code (e.g. 4W52) A project already created in Ligand-X
Step 1: Open or create a project
From the Ligand-X dashboard, click New project and give it a name. Your proteins, molecules, pockets, and job results will all live inside this project.
Step 2: Import your protein
In the project sidebar, click Proteins → Import. Paste a PDB accession code to fetch directly from the RCSB, or upload a local .pdb or .cif file. Ligand-X parses the structure and lists all detected components (chains, waters, ions, metals, co-crystallised ligands).
Step 3: Review detected components
The component panel shows every non-protein entity. Check which waters, ions, and co-ligands you want to keep or remove. Hover any component to highlight it in the Mol* viewer.
Step 4: Configure cleaning options
Click Clean protein to open the job form. Toggle the options you need: Remove waters, Remove ions, Add missing hydrogens, Fix missing residues (PDBFixer), Remove original ligands. You can keep co-crystallised metals when they are part of the active site.
Step 5: Submit the job
Click Run cleaning. The job is dispatched to the FastAPI gateway and processed by the protein-prep worker. A progress banner appears in the top bar; the job is also listed under Jobs in the sidebar.
Step 6: Review and use the output
When the job completes, the cleaned structure appears in the Mol* viewer. Check the summary panel for a diff of removed/added atoms. Click Download to save cleaned.pdb, or click Find pockets to proceed directly to pocket detection.
Expected outputs
cleaned.pdb — hydrogens added, unwanted components stripped Job record with input/output metadata in the project
Tips
If residues are missing from a loop, enable Fix missing residues before docking — gaps cause steric clashes. Keep crystallographic waters in the binding site if they mediate key contacts; disable Remove waters selectively per-residue.