Dear all,
I would to perform ligand docking in a volume that is defined by a ccp4 electron density map (Fo-Fc) at a given sigma instead of a standard regular grid.
Do you know some software that perform this kind of calculation?
Any suggestion are welcome,
Danilo
You can do ligand fitting with Phenix. There is an easy to use module in the GUI. If you have a structure of your ligand in some standard format, e.g. .pdb, and a file for restraints of bond lengths etc., then you can directly input these and run the ligand fitting module. If memory serves, it searches the difference map, but allows you to decide a cutoff based on correlation coefficient of what constitutes a solution. I would run refinements after automated fitting for several reasons, not the least of which is your electron density maps will improve and possibly reveal new features if your ligand was truly present.
I presume you are considering docking a novel ligand. In that case, prior to trying to search for the ligand in the density, you will need to draw it and generate a structure file. If you don't have software to do this, you can use https://cactus.nci.nih.gov/translate/ to do it for free. Just click "start structure editor" to start up the JSME structure editor and begin drawing. After you are done, you can get the SMILES string in a text file and choose from several structure file types (.sdf, .pdb, .mol). Once you have this, Phenix also has a module in the GUI called eLBOW that will automatically build a restraint file (in .cif format) that will be necessary for fitting and refinement. You have lots of options for how to generate the restraints, but default has worked for me in all but one case. There are similar ligand building/fitting options with CCP4 suite, JSCOFE (online CCP4), and others. I like Phenix, though. Hope that is helpful.
Thanks Matt,
Your answer are related to standard refinement procedure. Instead, I'm interested in docking procedure. Resolution of my data is too low thus structural details that we want are not tricky to get. The idea is to get more information by performing docking in a volume (not a grid as usual) defined to Fo-Fc map at specific sigma value.
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