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RosettaDesign Server, reproducing optimized interface conformation

Dear all,

I used the Rosetta Design server (http://rosettadesign.med.unc.edu) to search for mutations that stzabilize a protein-protein interface.
I have a two questions about this:

1) Is there any controll on the process, e.g., by means of a .res residue file, as is for the structure stabilization procedure? I seems like the settings in the .res file to not influence the PPIface stabilization procedure at all.

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protein-protien docking with uniform trans

Hello All,

I am attempting to dock two proteins and we have a general idea of the binding site on one of the proteins (protein 1) , but are unsure where the binding site of the second protein is (protein 2). We'd like to restrict the dockable area of protein 1 while leaving protein 2 unrestricted. I am trying to use the uniform trans flag. I did some testing/internet searching but I can't seem to understand exactly how its working. Here is the definition:

Uniform random repositioning of the second partner about the first partner within a sphere of the given radius, [R].

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Difference between relax and mimimize_with_cst

Hi all,

Reading the documentation of the ddg_monomer application I noticed that minimize_with_cst is needed to reduce collisions that result in a high free-energy score. For some structures I already used the relax application to achieve this. Hence my questions:

1. What does minimize_with_cst do? And how does it differ from what the relax application does?
2. Can I use my relaxed structure as input to a low res ddg_monomer run?

Looking forward to hear from you.

Cheers,
Bastiaan

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parameterizing new residues

Aim: ab-initio protein-modeling-docking for proteins containing non-standard amino acids .

I was able to parameterize the new amino acids for Amber ff, which developed along QM calculations for also K-Br atoms, i.e., at higher level than 6-31G* and DFT in place of HF. It worked: the MD simulation showed protein stability along 15 ns by using a NAMD-CUDA cluster.

Then, I collected info from Rosetta.3.3 forum, especially about mol2 file -> Rosetta parameters, such as in the thread initiated by einew on 02/28/2011 on "Rosetta applications".

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New files for loop modeling

Hi,

I have a question about new files for loop modeling - 650_LoopsKIC.py and T660_LoopBuilding.py .
I need generate N decoys and get N pdb files, and score them. How to implement these new files for that.
Do I need fragment files for loop generation if I use these files, like for old loop_modeling.py?
Unfortunately I did not find any reference for that.
What new features they have compare with loop_modeling.py ?

Thank you, Victor

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error during docking

Hello,

When I start running docking calculation (docking_protocol.linuxgccrelease), there was an error:

ERROR: total_residue() != 0
ERROR:: Exit from: src/core/pose/Pose.cc line: 1290

The command I used (just for test)t is:

dock -in:file:s ./prepack_protein.pdb -in:path:database $database -docking:docking_local_refine 1 -docking:dock_pert 3 8 -docking:spin 1 -docking:dock_min 1 -docking:partners [A_B] -docking:sc_min 1 -nstruct 50 -ex1 -ex2 -out:path:pdb ./path/ -out:file:scorefile ./path/

What's the problem? Or the prepack pdb file?

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Docking double-stranded DNA to a protein

I wonder if there is an example or tutorial for DNA-protein docking. How to prepare the file? Which command and flags to use?

My dsDNA is about 20 bps, protein has about 600 Aa. I would like to find the DNA interaction surface on the protein.

Any suggestion for other software, or sharing your successful experience would be highly appreciated.

Thanks!

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