Protein Preparation

Structures downloaded straight from the PDB are rarely ready for simulation. Flexible loops are often missing entirely, side chains can be truncated where density was weak, and hydrogen atoms are almost always absent altogether. Feeding a raw structure like this into docking, molecular dynamics, or FEP will produce misleading results at best or simply fail.

Rowan's protein-preparation workflow automates best-practice preparation techniques to get proteins fully simulation-ready. Under the hood, preparation happens in three stages:

Step 1: Rebuild missing residues and atoms

Rowan can fill in missing loops and side chains using either PDBFixer (a tried-and-true tool) or Boltz-2.

Boltz-2 is used here in an unusual way: rather than predicting a new structure from scratch, Boltz-2 refolds the polymer chains using the existing structure as a template, then relaxes the result with molecular dynamics to stay faithful to the original coordinates. This tends to do a better job than PDBFixer on difficult structures with long or heavily disordered missing regions.

Step 2: Assign protonation states

Once the heavy-atom structure is complete, Rowan predicts the protonation state of every ionizable residue and adds appropriate hydrogens. This can currently be done using either OpenMM's Modeller, protonate_utils, or PROPKA 3.

Step 3: Optimize hydrogen positions

Because the same heavy-atom structure and protonation states can support multiple different hydrogen-bonding networks, Rowan iteratively flips polymer side chains (His, Asn, Gln, and similar) to avoid donor–donor and acceptor–acceptor clashes, then runs a hydrogen-only molecular-mechanics relaxation to clean up bond lengths and angles.

The result is a structure that's fully MD-ready: complete, correctly protonated, and with a sensible hydrogen-bonding network.

Fully interoperable tooling

Protein preparation should be run on any protein before it's used in docking, pocket detection, molecular dynamics, or free-energy perturbation. Resubmitting from a prepared structure to a different workflow takes just a few clicks on Rowan's computational platform.

Ready to try it out? Create a free Rowan account and upload a structure to see it prepared in seconds.