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Question regarding Mlipo score

Submitted by DanielK on Tue, 2012-05-29 02:04

Dear all,

wanting to use the membrane abinitio application, I'd really like to know how the "Mlipo" score is calculated. I assume also using the .lips4 file as input? And is the .lips4 file used for anything else? I could not find this piece of information in the manual/forum and also not in the paper describing the membrane low-res. application (Proteins 2006, 62:1010).

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Rosetta 3 - General

how to pick fragments for a transmembrane protein

Submitted by tevang on Mon, 2012-05-28 06:52

Dear all,

I have created fragments with make_frags.pl script using the following command lne:
make_fragments.pl -verbose -nosam -nopsipred -nojufo -samfile UapA_SAM.ss2 -id UapA_ UapA.fasta

where UapA_SAM.ss2 is the SAM-predicted secondary structure in pripred_ss2 format, created in the following way:
ss_pred_converter.py --sam UapA.rdb > UapA_SAM.ss2

The UapA.rdb file has been obtained from ROBETTA server. Is this OK?

The default weight file used for fragment picking by "make_fragments.pl" script is the following:
# score name priority wght min_allowed extras

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Rosetta 3 - Applications

difference between score and bk_tot

Submitted by Lindsay on Wed, 2012-05-23 21:25

Deal ALL,
What's the difference between between score and bk_tot? The website says that "
score: the total score using the all-atom (high-resolution) energy function (lower is better)
bk_tot: total score used in the side-chain packing algorithm".
But I still confused. Which one the real energy of the protein structure? Is that lower bk_tot always has lower "score"? Thank you!

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Rosetta++ - General

rosetta3.4 fragment file problem

Submitted by David Hoover on Wed, 2012-05-16 14:42

In Rosetta 3.4, the fragment picker puts out a new format. AbinitioRelax does not recognize it. I get this error:

ERROR: no fragment to compute secondary structure
ERROR:: Exit from: src/core/fragment/SecondaryStructure.cc line: 68

If I run exactly the same command but with the old style fragment files, it works fine. Is there something I'm missing?

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Rosetta 3 - Applications

Protein Structure Prediction using PyRosetta, suggestions wanted :)

Submitted by oppopomoz on Tue, 2012-05-15 09:40

Hello!

Im trying to write a de novo folding script with pyrosetta (PyRosetta
v2.011 for windows).

I'm trying to follow the approach described in this paper:

Alena Shmygelska and Michael Levitt; Generalized ensemble methods for
de novo structure prediction, PNAS February 3, 2009 vol. 106 no. 5
1415-1420

that in turn refers to

Rohl, et all; Protein Structure Prediction using Rosetta, methods in
enzymology vol 383, 2004.

Right now I'm using only low resolution centroid score functions
because I'm not interested in the all-atom refinement stage in my project

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PyRosetta - Scripts

modeling missing linker in a protein

Submitted by Isaure de Beauchene on Fri, 2012-05-11 10:13

Hi,

What would be the most suitable procedure to model ab initio a long linker (~60 aas) between two protein domains, which structures and relative positions are knowns? This linker is missing in an X-ray structure of the protein, and has no homology in the pdb.

Is it possible to model the whole protein by homology on the X-ray template, build the linker, and then optimize only the linker while "freezing" the rest of the protein?

Thanks in advance,

Isaure

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Rosetta 3 - Applications

Speeding up docking to a large complex

Submitted by skovacs on Thu, 2012-05-10 20:50

Greetings,

I would like to dock a small protein (59 amino acids plus one 140 atom ligand) to a large trimeric complex (358 amino acids *per monomer*, plus eight 140-atom ligands). The total number of atoms in the system is nearly 21,000.
When I run a small test of the system using the following flags (we use Torque for queuing jobs) and generate 10 decoys per instantiation, each decoy takes between 1800 and 2400 seconds to complete (30-40 minutes).
command:
/pathto/bin/docking_protocol.linuxgccrelease
flags:
-in:path /pathto/rosetta_database/

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