PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations

Protein preparation is a critical step in molecular simulations consisting in refining a protein PDB structure by assigning titration states and optimizing the hydrogen bonding network. In this application note, we describe ProteinPrepare, a web application designed to interactively support the preparation of protein structures. Users can upload a PDB file, choose the solvent pH value, and inspect the resulting protonated residues and H-bonding network within a 3D web interface. Protonation states are suggested automatically, but can be manually changed using the visual aid of the hydrogen bond network. Tables and diagrams provide estimated pKa values and charge states, with visual indication for cases where review is required. We expect the graphical interface to be a useful instrument to assess the validity of the preparation, nevertheless the script to execute the preparation offline with the High Throughput Molecular Dynamics (HTMD) environment is also provided for non-interactive operations.