ProPrep: A Preparation Assistant for (Metallo)protein Simulations

ProPrep, a preparation program distributed with AmberTools26, orchestrates structure retrieval, assembly, alignment, curation, repair, simulation, and analysis for both soluble and membrane-embedded (metallo)proteins. ProPrep detects, parameterizes, and transforms specialized residues, including metal sites, modified amino acids, and organic cofactors into force field-compatible forms, and deposits the parameters into a user library for reuse. Sessions are recorded to a file so that work can be resumed, replayed, or repurposed for batch processing similar structures. In doing so, ProPrep serves both the newcomer learning the field and the expert working at scale.