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Add missing residues in loop modeling

Submitted by exchhattu on Thu, 2013-06-20 17:38

I am trying to use loop_modelling. I have small problem on my loop modeling problem. I have missing residues in protein. I gave these missing residues as blank in input pdb. My loop_modelling execution was successful however I did not solve my problem. I am wondering - can Rosetta add missing residues using loop modeling protocol? If so, how can be list of missing residues given in the program (parameter)? If not, could you please tell me any suggestion to put missing residues in the protein during loop modelling?

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Rosetta 3 - Applications

No pdb output file when running ab initio modeling

Submitted by bunyaviridae on Thu, 2013-06-20 01:33

I am using Rosetta3.4. When i run ab initio modeling, I only get a default.out and score.fsc files as output, even though I specify in the flags file that I want a pdb file as output. Also, my results file is seemingly incomplete, even though the run is complete in Terminal.

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PyRosetta - General

acceptable RMSD value in the clustered structures?

Submitted by ritacc18 on Wed, 2013-06-19 14:53

Hi,

I used Calibur to cluster my structures produced by Rosetta. And I got RMSD ~13 Anstrong within each cluster, to me it is very high.

And I'm wondering what's the common range of the RMSD within each cluster, that is acceptable ? (either clustered by Rosetta itself or Calibur)

And what's the algorithm to calculate the distance in the Cluster application of Rosetta?

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Rosetta 3 - General

how can we calculate Rosetta score on some decoy set?

Submitted by mirzaie on Wed, 2013-06-19 08:43

I need to calculate the Rosetta score(energy)on Rosetta All-atom Decoy Set and ITASSER Decoy set.

I will be grateful,if you guide me how can I do it or are there any papers that contain the

results of the Rosetta Program on ITASSER and Rosetta All-atom decoy sets?

Thanks in audiences.

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PyRosetta - General

non canonical aa mutations/force fields/pyrosetta

Submitted by Anouk on Wed, 2013-06-19 01:51

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!

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PyRosetta - General

interface_delta ligand_docking

Submitted by Prasanth Kumar on Tue, 2013-06-18 08:37

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?

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Rosetta 3 - Applications

SymDock for docking only the ligand?

Submitted by ast on Mon, 2013-06-17 09:53

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?

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Rosetta 3 - Applications

Does Rosetta scoring function can distinguish good structure from bad one?

Submitted by Victor on Sun, 2013-06-16 21:11

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.

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PyRosetta - General

A question on the logic of enzyme design

Submitted by agulsevin on Thu, 2013-06-13 08:10

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?

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