How to Quickly Prep Protein Structures for MD and Docking
Before running molecular dynamics or hydrogen-bond network analysis, a raw PDB structure needs careful cleanup first — and getting any step wrong skews the eventual conclusions. Water molecules can't be stripped indiscriminately, ligands need hydrogens added without creating steric clashes, and ions need their own handling. Tools like pdbfix help, but the process isn't a single simple pass.
What ChemOrchestra's Protein Refinement module does
Protein Refinement is one of ChemOrchestra's most-used modules, handling three tasks in one step: adding hydrogens to every entity (protein, DNA, RNA), stripping water and ligands where needed to simplify downstream docking, or keeping only ions when that's all that's wanted. Critically, the module also runs a short dynamics-relaxation pass on the output, so the resulting structure is already suitable as an MD starting point rather than a raw crystallographic snapshot.
Simple to run, meaningful cleanup under the hood
Usage is drag-and-drop: connect the refinement node, enter a PDB ID or load a local file (PDB or mmCIF both work). On a GDP/Mg2+-bound structure, for example, the refinement step clears out bulk crystallographic water while leaving the functionally relevant ion and ligand density intact and hydrogen-complete — the kind of cleanup that's tedious to do by hand but changes the reliability of anything computed downstream.
Pairs directly with Boltz-2 analysis
Downstream, ChemOrchestra's Boltz-2 analysis module automatically cleans up its own output structures and adds a pharmacophore analysis on top — so a refined structure can flow straight into co-folding and affinity prediction without a manual hand-off between tools.
How to do protein refinement: https://www.quantabricks.xyz/shared/dc15ee42-3776-4932-9ae3-a0e777fc67f9
Feel free to schedule a meeting with me if you have any specific questions/requests: https://calendly.com/yizhouma/chemorchestra-user-session
Join our community to learn more: https://discord.gg/u3Mb6C2aHv