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Protein Preparation Wizard — Refine Tab |
In this tab you can refine the assignment of hydrogen bonds, including terminal chi flips and histidines, remove waters based on their hydrogen bonding pattern, and perform a restrained minimization.
In this section, you can optimize the hydrogen bonding network and the orientation of Asn, Gln, and His residues, either interactively or automatically as a job. Both choices use the same underlying technology. A new entry is created for the optimized structure.
These optimizations are necessary because the orientation of hydroxyl (or thiol) groups, the terminal amide groups in asparagine (Asn) and glutamine (Gln), and the ring of histidine (His), cannot be determined from the X-ray structure. Flipping the terminal amide groups and the histidine ring can improve charge-charge interactions with neighboring groups as well as improving hydrogen bonding. The 180° flips preserve the heavy-atom placement deduced from the X-ray electron density. In addition, the protonation state of histidine is varied to optimize hydrogen bonding and charge interactions.
If waters are included with the protein structure, their orientations are also varied to optimize hydrogen bonding.
Select this option to sample water orientations when running the H-bond optimization. Deselect this option if the water molecules are already optimally placed, and you only want to run the other optimizations.
Use crystal symmetry when optimizing the H-bond network.
Perform a minimization for hydrogens that were adjusted during the sampling.
Perform the H-bond optimization with protonation states of residues at a given pH, as determined from a pKa prediction by PROPKA. The associated Label pKas option allows you to label the atoms in the protein with their predicted pKa values.
Perform the H-bond optimization with protonation states of residues in a given pH range. The options perform the following actions, relative to the normal biological pH of 7.
Run a job to optimize the hydrogen bonding network. The tasks include optimizing the orientation of hydroxyl groups, performing 180° flips of the amide groups of asparagine and glutamine and the ring of histidine, and adjusting the charge state of histidine residues. The job then orients water molecules to optimize hydrogen bonding. This is an iterative process, which passes over all the groups whose H-bonds need to be optimized multiple times.
Note: If you have a lot of water molecules in the structure, this process can take a long time. You should ensure that you have deleted unwanted waters before you start this process.
Opens the Interactive H-bond Network Optimizer panel, in which you can examine each assignment of terminal group or hydroxyl orientation and select the desired orientation.
Once the hydrogen-bonding network has been refined, you can choose to retain or remove waters based on the number of hydrogen bonds they form with parts of the structure that are not other waters. This allows you to keep waters that have significant binding to the receptor, for example, forming bridges, and remove the rest of the waters. To do so, choose the minimum number of hydrogen bonds from the Remove waters with less than N H-bonds to non-waters option menu, and then click Remove Waters. This is an alternative to keeping waters based on the proximity to the ligand, or manually removing waters.
This section provides controls for optimizing the corrected structure, to relieve any strain and fine-tune the placement of various groups. Hydrogen atoms are always optimized fully, which allows relaxation of the H-bond network. Heavy atoms can be restrained, so that a small amount of relaxation is allowed, or they can be kept fixed. These parts of the process are run as jobs under Job Control, since they are more time-consuming than the earlier parts of the procedure. A new entry is created for the minimized structure.
Specify the RMSD of the heavy-atom displacement below which the minimization is terminated.
Select this option if you want to leave heavy atoms in place in the minimization, and only optimize the hydrogen atom positions. Allowing some movement of the heavy atoms can relieve structural strain, but will result in some deviation from the input structure.
Select the force field to be used in the minimization. The default can be set under Jobs – Force field in the Preferences panel.
Perform a restrained minimization of the protein structure, using
impref.
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