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Docking

relax and movemap

Category: 
Docking

Can anyone suggest to me how to relax a protein with a non-covalent ligand? I want to make sure the ligand-binding site does not change dramatically.  In the following scenarios, which one looks reasonable:

1) relax protein with ligand; use movemap to exclude the rotamer of ligand residue 

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Rosetta Antibody Design: Error with foldtree: problem with the fold_tree:biggest_label != num_jump 2 1

Category: 
Docking
Design

Hi all,

I'm attempting to use Rosetta Antibody Design (RAbD) v2019.35.60890 to design antibodies for a protein whose structure is a trimer.
BACKGROUND: I can successfully run the RAbD protocol on the ful trimer structure from the PDB (6VXX) with the following command:

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RosettaAntibodyDesign] How can I use run_relax and run_snugdock as part of my command and workflow?

Category: 
Structure prediction
Docking

I am trying to run a basic antibody/antigen design/dock simulaton using RosettaAntibodyDesign (from Rosetta 3.12)

I am using the command:

antibody_designer.macosclangrelease \
  -database /path/to/database/ \
  -do_dock \
  -use_epitope_constraints \
  -nstruct 5 -in:file:s complex_renumbered.pdb \
  -seq_design_cdrs H1 H2 H3 \
  -primary_cdrs H3 \
  -mintype relax \
  -run_snugdock \
  -run_relax \
  -out:path:all ./output 

 

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How to fold-and-dock in PyRosetta?

Category: 
Structure prediction
Docking
Symmetry
PyRosetta

I'd like to do something similar to regular Rosetta fold-and-dock but in PyRosetta.  I've looked at D060_Folding.py and D100_Docking.py examples and while I (mostly) understand what each is doing, I have no idea how to combine them.

How to get a foldtree with symmetry? (in my case it's just simple C3) 

How to combine folding and docking?  Just alternate calls to folding.apply(test_pose) and dock_prot.apply(test_pose)?  (It can't be that simple...)

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Transmembrane helix fold-and-dock?

Category: 
Structure prediction
Docking
Symmetry
Membrane

I'd like to fold-and-dock a trimeric transmembrane domain.  I mostly have the "Fold And Dock" working following the example in demos/public/symmetry_examples/fold-and-dock/.  However this is treating the transmembrane helixes as though they are in solvent (so for example any hydrophilic groups always rotate outwards).  I'd like to do something which is a combination of "Membrane Abinitio" and "Fold and Dock".  Is this possible, and how do I do it?

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How to specify constraints during fold-and-dock?

Category: 
Structure prediction
Docking
Constraints
Symmetry

I'm folding a protein which is a trimeric long helix bundle.  I started from the main/demos/public/symmetry_examples/fold-and-dock/ and added my info (sequence, fragments etc).  This basically works but a lot of the resulting folds are globular not long - the helixes fold over on themselves.  I'd like to constrain this to extended conformations only.

I looked at constraints in the Rosetta docs, and tried creating input_files/constraints.cst to give a penalty to any structure which has less than 50-70 A distance between residues 1 and 63:

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General question regarding ligand-docking

Category: 
Docking

I am quite new to Rosetta. I have a very simple questions regarding general concepts about ligand-docking. I am a little bit confused about how to set parameter to ensure that all conformers generated can be tested. Lets say if I have a PDB containing 50 conformers. If I set -nstruct = 1 and run docking.xml with transformer like this (Transform name="predock" chain="X" box_size="20" move_distance="2" angle="20" cycles=“500” repeats=“2” temperature=“5”/>). What does really happen through the docking simulation? 

 

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ligand docking error

Category: 
Docking

Dear all:

I am a beginner of Rosetta. While I am running ligand-docking toturial (https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial). I encounter an error when run script calculate_ligand_rmsd.py when doing data analysis. This script is used to calculate RMSD of each model comapred with the best model. When I run this script, the error indicated :

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