drug-protein-prep

You can prepare a protein receptor for docking by fetching an RCSB PDB ID or loading a local file, then using PDBFixer and OpenMM to clean missing residues and add pH-specific hydrogens for a ready structure.

Yes, you can add hydrogens to a PDB file at a target pH using PDBFixer and OpenMM, which protonates the cleaned receptor structure to satisfy specific docking workflow requirements for AutoDock Vina.

PDBFixer supports optional chain selection and biological assembly selection when preparing receptor structures, allowing you to isolate specific protein chains from RCSB PDB or mmCIF inputs for targeted docking preparation.

You can convert a prepared receptor PDB to PDBQT format using the MCP Meeko-based conversion tool, which delegates the format generation step to satisfy AutoDock Vina docking workflow requirements after initial PDBFixer cleanup.

The best way to fix missing residues and nonstandard residues in a protein structure is using PDBFixer with OpenMM, which repairs structural defects and handles heterogens or water during the receptor preparation process.

Raw PDB structures often fail in docking simulations because they contain missing atoms, nonstandard residues, and absent hydrogens, which must be cleaned and protonated at a target pH before successful molecular docking.