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I have two questions concerning conformers in the enzyme design application:
1) Is hydrogen bonding calculated from heavy atoms only or should the conformer library contain, for example, hydroxyl groups with the hydrogen pointed in multiple directions for it to recognize when a hydrogen bond can be formed?
I see some strange behavior of enzyme design with ligand.
1) I have created a library of rotamers, set path to this library in params file (by PDB_ROTAMERS rotlib.pdb) and run enzyme design. But there is still only translation and rotation of rigid body in the active site and no using of the rotamer library. Only when I start with ligand structure with some clashes in the protein pdb file I can see optimization of of torsion angles of the ligand. Can you please explain how it works?
Is it possible to combine a flags file with command line arguments?
For example, something like this:
minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file
where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:
minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list
I would like to know whether the enzyme design protocol of Rosetta Suite can be used for increasing the catalytic activity of the enzyme. Here, I don't have to design the active site from scratch, but I need to design the active site in such a way so that the catalytic activity of the enzyme is increased. Also, the enzyme I am dealing with does not have data for transition state modeling for the substrate that I am dealing with.
Please provide you comments and suggestions
I try to find public paper which use Rosetta as a method, but I can not see. If you have read any paper have used Rosetta protocols , please give me some.
Thank you so much