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membrane protein packing prediction

Submitted by djpittdj on Fri, 2012-01-13 08:55

Hi, fellows:
We have two transmembrane peptide from two separate membrane proteins and we would like to see how they pack. The conformation of helix 1, i.e., tilt angle w.r.t the membrane etc, is determined by NMR. For the second helix, we currently take it as an ideal helix. The tilt angle for helix 2 is also known. This problem is similar to the glycophorin A packing problem addressed in "Toward high-resolution prediction and design of transmembrane helical protein structures".

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Rosetta 3 - General

using defined WATERS in PACKING

Submitted by ast on Wed, 2012-01-11 09:11

Hi,

does anybody have experience or ideas on how to involve waters in a packing/design process?
I want to repack a protein but want to make sure to include some water filled cavities. Is there a way to define waters or a sort of placeholder, though explicite waters would be better, so that the design-packer can generate a suitable surrounding.
Thanks!

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Rosetta 3 - General

Reading and writing structures using streams

Submitted by Lior on Mon, 2012-01-09 09:05

Is there any way to read (write) structures (pdbs) using a python stream?
Couldn't find any clue in PyRosetta's documentation, so I guess its not a standard feature.. but I'm wondering whether there's a hack people use to in order to enable it..

Thanks!

Lior Z.

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RosettaHoles

Submitted by ge0rgekh0ury on Mon, 2012-01-09 09:01

Good Afternoon,

We were wondering if Rosetta3.3 had the ability to use scoring as described in

RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation by Will Sheffler and David Baker

We have searched the forum for how to utilize it but were not able to find a solution.

Any help would be greatly appreciated.

Best,
George

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Rosetta 3 - General

creating a pose from a pdb style string

Submitted by mmertens on Fri, 2012-01-06 01:01

hello,

is there any possibility to create a pose from a pdb style string in pyrosetta?

from the "PyMOLPyrosettaServer.py" script I can see that pymol can be made to listen for a pdb string sent from pyrosetta. i would like to go in the other direction directly passing a pdb string to pyrosetta in order to generate a pose. is this possible? and if so what is the necessary code for this?

i know that one can generate a pose from a pdb file but i would like to skip this step in order to save the time it costs to read/write from/to disk.

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PyRosetta - Scripts

Difference between score and silent_score when silent files are combined

Submitted by justin on Tue, 2012-01-03 06:44

Dear all,

I am using rosetta3.2 membrane_abinitio2 function to predict some membrane protein with 4 TM helices.
I split the prediction into 10 independent runs and each run resulted in 2000 decoys in a silent file.
When I combined these 10 silent files together, I find that the "score" changes.
Here is the score profile before combination:
SCORE: score vdw Mpair rama Menv Mcbeta Menv_non_helix Menv_termini Menv_tm_proj Mlipo hs_pair ss_pair rsigma sheet co clashes_total clashes_bb time description

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Rosetta 3 - General

RMS in Score Application

Submitted by brspurri on Thu, 2011-12-29 09:19

Hi all,

I am using the score.linuxgccrelease application to score my silent file (containing 20,000 structures). I am also using the -native flag to calculate an RMS for each of these structures. (I'm trying to get an RMS vs Score plot).

I am using the command:
score_jd2.linuxgccrelease -in:file:silent P001.silent.all -out:file:silent P001.silent.all.scored -out:file:silent_struct_type binary -in:file:fullatom -database $ROSETTA_DATABASE -out:file:scorefile P001.score -native ../../master/template_master.pdb

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