Protein Preparer

Clean predicted or experimental structures with PDBFixer, protonate at a chosen pH with PDB2PQR and PROPKA, and emit a dock-ready PDB plus receptor PDBQT — without solvation or MD equilibration.
Estimated minimum cost: $—

Examples

Input

Provide a PDB ID or upload a protein structure (PDB or mmCIF). Fold jobs such as ESMFold2 and Boltz-2 chain in as CIF or PDB.

Protein structure

Preparation options

PDBFixer adds missing heavy atoms. PDB2PQR and PROPKA assign hydrogens and titration states at the given pH. Waters and HETATM ligands are independent flags — long missing loops are not rebuilt.