Third, each of these placements is taken as a starting point for fitting the remainder of the ligand. The defined site then may be edited, saved and later restored for further study. Occasionally, if none of the candidate ligands in the library can fit the electron density well enough, especially when the density is much smaller than the ligands to be tested, the program will return an empty list. If phases are to be read in then MTZ format is required. Only applicable if there is one type of ligand. LigandFit will start several child processes to sample a wide variety of ligand conformations. 
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Values significantly higher than 0.
Automated ligand fitting with LigandFit
A value between 0. I know the chemical name lkgandfit my molecule, but I don't know what residue name has been assigned in the PDB. If this file contains atoms other than waters in the position liganxfit the ligand is to be built, then you may wish to remove them before building the ligand. The ligand file can be a PDB file with 1 stereochemically acceptable conformation of your ligand.
Protein atoms overlapping with the ligand density will prevent a successful placement, so some editing of the input structure is generally recommended.
Water molecules will be automatically removed if necessary. See the list of keywords, defaults and descriptions at the end of this page and also general information about running Wizards at Using the PHENIX Wizards for how to do this. Then you can edit this file and run it with:. Before displaying the results in graphics, is there a way to know if the program finds anything interesting?
Multiple ligands The Fit Ligands control panel can also be used to dock multiple ligands or multiple conformations of ligand s into the binding site of the same protein by loading the ligands from an SD file.
Tutorial: Fitting a flexible ligand into a difference electron density map
Does it have clear density for the ligand? This will prevent you from applying anisotropy corrections, however. It is okay for this to contain previously-placed ligands as long as the intended binding site is empty. These will be used to exclude that region from consideration.
Unless quick mode is enabled, LigandFit typically works by starting multiple similar jobs with slightly different parameters, to sample as many candidate ligand conformations and density fits as ligandgit.
After all iterations are completed for the remaining saved and docked conformations, a rigid body minimization using the BFGS procedure is performed.
If you do not obtain a good fit of your ligand to the map, there are a few things you should check: Run on a queuing system: If you want to get the same results, keep the same value of nbatch. After the first round of calculation, the energy grids are available for subsequent ligand fitting.
You can run phenix. How can I fix this? Automated ligand fitting by core-fragment fitting and extension into density.
If LigandFit was unable to place the ligand correctly, there are several recommendations for troubleshooting:. Not available on Windows. Checking Use distance dependent dielectric constant indicates that the distance dependent dielectric constant is used in the standard electrostatic energy calculation.
However, if you are using pre-calculated map coefficients, you may need to remove waters beforehand to avoid "flattening" the difference density around the ligand. The LigandFit Wizard excludes all ligandfih that are occupied by atoms in the oigandfit model.
If you leave nbatch as None it will be set automatically, with a value depending on the Wizard. Note that you can, optionally, set the Energy Grid Preferencesincluding: The defined site then may be edited, saved and later restored for further study. In any case, you should always visually inspect the ligand placement in Coot, both before and after refinement. A shape comparison filter is combined with a Monte Carlo conformational search for generating ligand poses consistent with the active site shape.
Automated ligand fitting with LigandFit
No translation or rotation is performed. Is there anything strange or unusual in any of them that may give you a clue as to what to try next? All of these can be opened at once in one of the graphics programs by clicking the buttons next to the file list.
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