The problem hasn't been solved
Hi all,
I'm new to PyRosetta and just had a quick question !
I have a protein and need to compute the energy, then to acetylate certain Lys, repack after the replacement and recompute the energy. I am wondering how is the score function name (is it mm_std?) and also where can i find non canonical aa codes. THANKS!
Hi,
In liganddock documentation, it is said "interface_delta" (in score.sc ) gives estimate of the binding energy.
Can this be related to experimental units of binding energy i.e like in terms of kJ/mole?
Are there any experimental evidence to show that the "interface_delta" correlates with that of the experimental binding energy?
Hi everybody,
another symmetric docking question. What I want to do is symmetrically dock two ligands to a receptor dimer, the binding sides are between the two symmetric interfaces (its the tryptophan repressor dimer binding two tryptophans). When I try SymDock it docks the monomers, as its supposed to be, albeit not in the right way (the crystal structure). What I basically want is just symmetric ligand docking, it should leave the interface from the .sym file untouched, apart from minor adjustments if necessary. Maybe SymDock is the wrong approach in this context?
I use standard KIC script for a loop modeling by PyRosetta. However in some cases the generated loops do not have appropriate structures, especially in the middle of the loop, were the cut point is. Typically, I get loops with a good structures, however in several cases the loops have a bad chemical connections or even broken structures in the middle of these loops.
I wanted to filter out these structures using Rosetta standard scoring function, but all scores for bad structures are in the same range or even better than the energy for good structures.
Hello,
I am trying to use enzyme design app in Rosetta 3.4 with a small ligand docked into an enzyme (no enzyme-ligand covalent connection), and I have two questions about it.
The first is, I do not know which residues of the protein take part in the catalysis, so I cannot form a .cst file. Would results of such an enzyme design job without a .cst file be somewhat reliable or total rubbish? What else could you suggest me to do about it, is there any way to compensate the absence of such catalytic knowledge, or is the program only designed to work with appropriate catalytic constraints?
Dear friends
i am trying to run script "clean_pdb.py" but its not running and showing error massage....
how can i come out of it.. Please help
hi all,
I want to create a peptide with N-term N atom unprotonated and C-term C atom protonated.
like NH2-ALA-GLY-PRO-COOH
How to do that?
Thanks.
Hi all,
I did ab initio modeling with rosetta and then performed clustering. Initially I generated 500 decoys and then I did 1000 with a difference sequence. When I performed clustering, I still get 4 clusters yet I have not specified the number of clusters in my flags file.My question is whether this is a correct output?
Hi there,
I am trying to dock DNA to a protein (2 chains; it's a dimer), and to the best of my knowledge, there's not an out-of-the-box application that does this (there is another thread on here about that). However, I have used the RosettaScripts RosettaDNA design demo successfully, which reads, designs and scores a Protein-DNA interface.
Hi Dears,
I preformed using fragment-based loop modelling to model and get a 8 residue helix on the loop.
I generated 1000 models, now I want to filler my models to get a model with a helix on the loop,
Would you please let me know, how to find my mentioned model (i.e.,including a helix in loop area) among 1000 models.
Thanks in advance,
Ramin