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RE: Loop Modeling and Beta-strand design

Submitted by bharat_46010 on Sun, 2012-02-12 16:34

HI,

I am interested in mutating some loop residues together with the residues of the beta-strand , the loop is connected with. In such case what has to be done?.. Does fixedbb design will work in this case ??

Also , I have another query regarding Rosetta Scoring. I want to test all the 20 possibility of amino acids at two loop residues (20*20=400) of a beta hairpin . In that case will there be any large change in energies of a pair of combination of amino acids ??

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Rosetta 3 - General

Cannot get PyMOL_mover to work on MacOS

Submitted by cno on Fri, 2012-02-10 07:24

I've trying to set up the PyRosetta PyMOL viewer on a MacOS 10.7.3, 64 bit system, but I cannot get PyRosetta to send graphics(?) to PyMOL. The current setup is:
PyRosetta 2.011 [r46035]
Python 2.7.1
PyMOL 1.5.0

I start PyMOL:
PyMOL>cd /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit/
cd: now in /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit
PyMOL>run /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit/PyMOLPyRosettaServer.py
PyMOL <---> PyRosetta link started!
at 127.0.0.1 port 65000

Running through the walkthrough in Baugh et al I get:

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PyRosetta - General

RosettaDesign Server, reproducing optimized interface conformation

Submitted by AlexanderMetz on Thu, 2012-02-09 10:41

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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Rosetta 3 - General

protein-protien docking with uniform trans

Submitted by lkingsle on Thu, 2012-02-09 07:19

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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Rosetta 3 - General

Difference between relax and mimimize_with_cst

Submitted by basvandenberg on Thu, 2012-02-09 00:16

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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Rosetta 3 - Applications

parameterizing new residues

Submitted by chiendarret on Fri, 2012-02-03 22:59

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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Rosetta 3 - Applications

New files for loop modeling

Submitted by Victor on Fri, 2012-02-03 14:36

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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