Upon completion of this project, we will provide updated structural files (PDB, mm/CIF, MOL2) for each of the explored conformers/states/modes along with the corresponding MTZ file for each mode (if an X-ray/cryo-EM-based project is requested). You will also receive a detailed report and "tarball" with the various states along with a score for each to allow you to decide which state is more correct than the other states considered. We support the following structure preparation options:

Bulk Protonation: Generally, when a structure is first obtained from a crystallographer, protonation has not been performed. QM, MM, and QM/MM are "all atom" methods meaning that accurate protonation states are required for the entire molecule. As part of the preparation process, we will protonate the entire structure using our built-in tools.
Refinement/Optimization: Often initial crystal structures are highly strained due to the use of stereochemical restraints during a conventional refinement. Our method uses a QM/MM functional for refinement/optimization. Further, if complete experimental data is supplied, this data will be supplied to our built-in real-space refinement functional and the resulting crystal structure will exhibit lower strain, improved interaction energies, and often improved agreement with density.
Ligand Placement / Docking: With XModeScore coupled with our built-in free energy (MovableType) docking routine, we are able to explore ligand placement. Currently, experimental density is required for this function to be used effectively.
Ligand Tautomer/Protomer Enumeration: XModeScore was first built to explore protonation states of the ligand(s) and surrounding active site(s) utilizing a combination of density and the QM/MM potential to choose the correct state or states in the ligand.
Ligand Flip State Selection: In conventional X-ray crystallography, atoms such as carbon, nitrogen, and oxygen are hard to differentiate. MM and QM on the other hand are highly sensitive to the different chemical properties of these elements. With XModeScore, we can accurately determine the flip state of the ligand(s) in the structure.
Ligand Stereoisomer Selection: If your ligand has one or more chiral centers, sometimes conventional crystallographic methods exhibit difficulty in determining which stereoisomer is bound within the active site. XModeScore is used to determine which ligand is bound to your active site.
Bulk Solvent Addition: Using technologies available at QuantumBio, after placement of the ligand, we can update or rebuild the bulk solvent of the model exploring any available density. Note: bridging water site locations within the active site will generally be explored regardless of this choice.
Target Rotamer Selection: XModeScore can also be used for the target structure to determine which disordered rotamer is more correct within the target according to both density and the QM/MM interaction energy.
BIOUNIT Construction: In order to construct the BIOUNIT, your provided input must include the BIOMT1 records.