You are here
I was running the integration test of the enzyme design (main/tests/integration/tests/enzdes). According to the fifth constraint block in the cstfile at position Trp100 residues WFY with atom type aroC are allowed. However within 150 output structures I never observe a mutation away from the native Trp. In contrast, residue Ser98 is variable in the results (only has backbone constraints). Similarly, I never observe any mutation away from a native catalytic sidechain in my own project.
I experience difficulties when submitting an enzyme PDB file with the
substrates AMP and a non-proteinogenic amino acid to the RosettaDesign webserver.
AMP is well accepted but problems arise with the amino acid substrate.
Hey, I am pulling my hair out over this. I am trying to convert all residues in a protein to poly-Gly/Ala (for example 1ae1.pdb) but cannot find the Rosetta function to do so. I am replicating a paper where they included code and output, the output appears to be typical Rosetta output (the .pdbs are like 3tzc___1.pdb) which I am assuming were generated with a Rosetta function.
I used Enzyme Design application to get a series of enzymes with ligand(transition state of my target reaction). Now I want to inspect the free energetic change upon the protein transition state binding.
So I first look into the ddg_monomer application, and I find this application is suitable for comparing ddg energy between wild-type protein and its mutant structures. This can't meet my needs.
So I have not been in the Rosetta world for very long, and most of what I have learned I have had to parse from the Rosetta Commons Demos/Documenation and various publications since no one else at my institution does this sort of work. So while I have learned quite a bit, there is some fundamental questions about approach/methodology that I feel blind towards.
I want to refine a PDB file with one zinc ion using 'SetupMetalsMover'.
I have added one zinc ion which is predicted to coordinate with cysteine and histidine.
I noticed there is 'CYZ.params' file and 'residue_types.txt' file ( '/database/chemical/residue_type_sets/fa_standard/residue_types.txt' file ) includes the 'CYZ.params'.
Then, I changed the residue name of cysteine to 'CYZ' (from CYS).
And then, I executed rosettascript to refine my pdb.