The problem hasn't been solved
Dear community,
I had this posted under a different sub-forum but I realized it didn't fit that forum so deleted it and reposting here.
Hello,
I'm working on de novo enzyme design. Utilizing the enzdes application through theozyme definition. While doing regular design procedures I have noticed that Rosetta inserts amino acid identities that create clashes with the ligand. Most notable is an Ile with a distance of 3A to the ligand, instead of the minimum 4. Images attached. As far as I know, I have not altered the default behavior of vdw radii at any point. The energies for these residues do not sky-rocket and Rosetta scores these designs very favorably.
Dear friends,
I am new to rosetta and need some help. Basically, I have two questions:
1) My main interest is to use rosettafold to predict structures. Do I need to install pyrosetta for this purpose?
Hello all - brand new to using pyrosetta so apologies if I'm missing something obvious.
Hi all! I am attempting my very first enzyme design campaign and running into issues with matching. I generated a cstfile from averaging native pdb measurements within a family, and am trying to match my theozyme (a new substrate - LFF) to one representative structure as a test (PDB ID: 5nci chain A).
When I run:
Dear all,
I generated a silent file as a result of a docking refinement with FlexPepDock. I want to anaylize the top 10% of the solutions (1000 decoys) and cluster them.
First, I extracted the top 10% by sorting the I_sc with:
sort -n -k2 example_score_file.sc | head -n 1000 | awk '{print $2 "\t" $25 "\t" $NF}' > score_I-sc_tag.dat
Hi, looking for some help,
It appears that constraints do not contribute to the final score output when running the FlexPepDock ab initio protocol.
I am getting docking samples that should yield score penalties >1000 under the provided distance constraints (AtomPair FLAT_HARMONIC). However, the scorefile reports numbers consistent with the score absent of penalties (approx -550, for a protein length 300 and peptide length 5).
I provide the constraints file with the flag -constraints:cst_file
Hi there,
I've noticed that the FlexPepDock ab initio protocol will run even if fragments aren't specified. It also appears during these runs that the peptide backbone is flexible, varying between samples.
When no fragments are specified, what does the FlexPepDock application do to ab initio model peptides exactly?
Is there a 'default' set of fragments?
Thank you!
Nathan