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Docking

dG_separated threshold for identifying non-binding peptides with InterfaceAnalyzer.

Submitted by jyotisutar9 on Thu, 2016-12-01 00:39
Category: 
Docking
Scoring

Hello,

I am a beginner in protein modelling/analysis and trying to learn through tutorials and the forums here.

A bit of a background of my present Task: I have a crystal structure of an Ab-Ag complex (AbFab with Ag peptide). I also have experimental data on binding affinities of several Ag peptide variants. I want to use this data to predict binding ability of novel Ag peptide variants with the same Ab.

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Rosetta 3 - General

Changing the Number of Cycles of D110_DNA_interface.py Script

Submitted by mrodr26 on Mon, 2016-10-24 11:33
Category: 
Docking

Hello,

I am trying to create docking poses using D110_DNA_interface.py.  For my application I do not need extremely accurate poses (RMSD<0.5) to be created, is there anyway to limit the number of cycles the scripts runs through to create a pose? Ideally, I want to create poses in the range of RMSD between 1-20 angstroms. 

I tried using the "Custom docking" commands in the same sample script to change the number of cycles but get the following error:

AttributeError: 'DockMCMCycle' object has no attribute 'get'.

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PyRosetta - Scripts

Ligand Docking with Orphan GPCR

Submitted by marsaa on Thu, 2016-10-13 07:45
Category: 
Docking

Hi all,

I've recently started to use the Rosetta suite for some basic modeling of an orphan GPCR. Our research group has discovered several compounds that interact with the membrane protein, either directly or indirectly. To see if any of these compounds could act as ligand, I turend to the ligand-dockng protocol. I went through the tutorial (with some issues) however the results were succesful. Now that I am trying to do it with my orphan GPCR, i've run into some issues:

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Rosetta 3 - General

DomainAssembly Mover with constraints (using RosettaScripts)

Submitted by resiros on Wed, 2016-09-21 11:19
Category: 
Docking
Scoring
Constraints

Hello,

I am trying to run the domain assembly protocol while atom_pair constraints . I am using RosettaScripts for my application.

I have tried including the constraint file in the xml script using the ConstraintSetMover and Reweighting the score function. I have also tried included the constraint file in the flag file using -constraint:cst_fname. Yet the output silent do not seem to include the atom_constraints score term.

I would appreciate any help on how to include the constraints in the scoring function for domain assembly.

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Rosetta 3 - General

why is talaris2014 scoring fuction not used with ligand docking?

Submitted by banshee on Fri, 2016-09-09 01:19
Category: 
Docking

hi

someone who uses rosetta ligand docking protocol was asking why score12 was used for ligand docking and not the most recent scoring function which i believe is talaris2014? is it just because it has not been tested yet? or for some other reason? thanks.

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Rosetta 3 - Applications

dock & design

Submitted by sdh_h on Fri, 2016-09-02 03:07
Category: 
Docking
Design
Constraints
Symmetry

Dear All,

I would like to simultaneously dock and design two (or more) identical subunits into a a symmetric homooligomer.

Input:

- backbone structure of a monomer (no sidechains!);
- initial arrangement of the subunits;
- constraints that precisely define interactions between the subunits.

Simulation:

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Rosetta 3 - General

Difficulties with Protein Docking using Harmonic Restraints

Submitted by Parker.deWaal on Fri, 2016-08-19 11:23
Category: 
Docking

Hello Everyone,

While trying to use harmonic, or guassian, distance restaints in low resolution centroid only docking in the docking_protocol.linuxgccrelease I've encountered weird Scoretype: atom_pair_constraint score errors that prevent the output of docked proteins.

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Rosetta 3 - General

Error using pHDock

Submitted by SenyorDrew on Thu, 2016-08-11 05:56
Category: 
Docking

Hi,

I'm having trouble running pHDock (in an attempt to model protonated histidines).  I'm using the command-line arguments described in the pHDock paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263365/):

~/rosetta/bin/docking_prepack_protocol.linuxgccrelease -s input_prep_sc.pdb -partners AB_C -dock_ppk -pH:pH_mode -pH:value_pH 5.6 -score:weights packing.wts -ex1 -ex2aro -unboundrot input_prep_sc.pdb

Fails with the error:

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Rosetta 3 - General

Docking-Error 500

Submitted by edebenedictis on Wed, 2016-08-03 12:34
Category: 
Docking

Dear all,

I submitted a protein-protein docking job (24902) and kept track of it through the queue.  I recently was emailed when it completed, but anytime I try to access the job page, I see the message: "Error 500 We're sorry but we weren't able to process this request."  This is both accessing from the link in my email, and from the ROSIE queue.

Please let me know if there is anything I can do to resolve this, or if I should just resubmit the job.

Thank you,

Elizabeth

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ROSIE - General

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