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Ab initio peptide design to use as ligands in docking

Submitted by archaeopteryx on Tue, 2023-06-27 11:09
Category: 
PyRosetta

I need to create peptides to use them as flexible ligands in docking (DockThor platform). I'm new at pyRosetta so I've only seen 1 tutorial until now. I'm using the following code

import pyrosetta
from pyrosetta import *
from pyrosetta.toolbox import *
init()

peptide_sequence = 'insert peptide sequence'
pose = pose_from_sequence(peptide_sequence)

scorefxn = get_fa_scorefxn()

# define variavel score before relax
score_before_relax = scorefxn(pose)

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PyRosetta - Applications

Generating a new Vall database

Submitted by vijay.anand on Tue, 2023-06-20 12:08
Category: 
Fragment Generation

Hi, I've been looking through the fragment-picker application and my objective is to select fragments from the vall database such that only fragments that are 100% identical to the query fragments are selected. Since the probability of getting larger fragments, that are entirely identical to the query fragments, is low; I wish to create a newer updated vall database from more recent and bigger protein databases. Could someone guide me through achieving this task or point me to the required references?

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Rosetta 3 - Applications

Different results FastRelax pyrosetta vs rosetta_scripts

Submitted by karenjgonzalez on Tue, 2023-06-20 09:52
Category: 
PyRosetta

Hi everyone,

I want to relax a designed disulfide bond with FastRelax, but when I try to do it in Pyrosetta it seems like it gets no optimization at all. However, when I try FastRelax in rosetta scripts I get a good geometry. Could you please help me identify what I am missing in my Pyrosetta code?

Thank you!

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PyRosetta - General

Questions about gen_apo_grids

Submitted by JasonIsaac on Sat, 2023-06-17 00:20
Category: 
Docking

Hi, everyone:

    I want to generate pos file for different scaffolds, and I find that gen_apo_grid can satisfy my needs. But there is a problem, if this option "-packstat:surface_accessibility"  is on, I can set the value of "-packstat:min_surface_accessibility". Whatever value I set for "-packstat:min_surface_accessibility", the output pos file does not change at all. 

Example Command Lines: 

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Rosetta 3 - General

Silent File Scores Missing: RNA Protein Complex Predition

Submitted by axio23 on Fri, 2023-06-16 05:45
Category: 
Nucleic Acids

Dear Community,

I am relatively unexperienced with Rosetta and am for the first time trying to run the Protein RNA Complex Prediction Tutorial, as described on the website and the readme file using the latest weekly Ubuntu release. So apologies if I did a newcomer mistake.

When running as described, I get an error that I need to add the option base bair steps to false, so I added

-bps_moves false

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Rosetta 3 - Applications

Compilation and Setting up Rosetta

Submitted by Pj on Fri, 2023-06-09 21:38
Category: 
Compilation

Hello, I have had some problems with the compilation of Rosetta. I'm using Ubuntu 22.04.2 LTS. For compilation I used the release mode.

When I type: ./scons.py -j1 mode=release bin (OR) ./scons.py mode=release bin, I'm getting the following error:

 scons: Reading SConscript files ...

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Rosetta 3 - Build/Install

non-zero ddG of binding even without mutations

Submitted by top-gun98 on Wed, 2023-06-07 17:19
Category: 
Design

Hello,

I was trying to work with the "calculate protein-protein ddG" tutorial. The tutorial comes with a resfile for mutating an Alanine with Tryptophan at residue 98. Following the steps gives, I get a ddG value of -6.6533 REU.

However, when I replace the line "98 D PIKAA W" with "98 D PIKAA A" (i.e. esentially replacing the alanine with alanine), I'm still getting a ddG value of 6.6643 REU. Can anyone point out why I might be getting a non-zero ddG even though I'm not even 'mutating' the proteins.

Regards,

top-gun98

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