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Loop Modeling

Fusing C-terminal or N-terminal segments onto proteins using Remodel

Category: 
Design
Loop Modeling

Hi, I am trying to replace the C-terminal segment of a designed protein with that taken from a crystral structure using the Remodel module with the DomainFusion flag turned on. I have tried several different tweaks to the arrangment however the gist of it is that I use the following command. 

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RosettaScripts - FastRelax loops

Category: 
Loop Modeling

Hi all,

I am using RosettaScripts for some loop modelling and would like to apply the FastRelax protocol to a loop region in my structure without the moves propagating down the chain.

I know that it is possible to set up a MoveMap so that only some degrees of freedom are turned on e.g.

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docking with constraints and flexible bb

Category: 
Docking
Loop Modeling
Constraints

Hi,
I am doing unbound docking and i believe I have enough biological info to locate the binding interface and rough orientation. Doing the docking manually (or with the low res protocol) suggests that there's some conformational change in the interface that I would like to model. I'm guessing this is not something that I can accomplish with the old docking_protocol commandline app. I did see a flexible_bb_docking option but that appears to be undocumented? Maybe I can do this via the ensembles options?

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auto_setup_metals flag with loop modeling application fails

Category: 
Loop Modeling
Constraints

I'm trying to make a homology model for a Zn-binding metalloenzyme based on some other members of the same family that have been crystallized. My general strategy has been to do comparative modeling first with limited redesign of the loops to get the main structural features in place, and then use the loopmodel appliation to refine the structure a bit more. I had trouble incorporating the Zn residue into the comparative modeling application, so I inserted the Zn into the PDB result and now I'm trying to include it in the loop modeling step.

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loop modeling scoring

Category: 
Loop Modeling

Hi, everyone. Recently I'm using Rosetta to perform the modeling of a loop region. But when I check the score.sc file, I got several values that are extremely high. I don't know how rosetta perform the scoring of these models. Is it due the clash of atoms ? Does it mean that this conformation is bad and should not be taken into consideration ? Besides, I want to convert the rosetta energy into physical energy unit (kcal/mol) ? How can I perform this ? Can anyone give me some tips ?

Thank you very much

Nicky

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Minimization Issue: Coarse Graining to All atom modeling

Category: 
Docking
Design
Loop Modeling

Hi all,
I want to get an all atom model of my coarse grained protein structure (after adding all the side chains back). I have been using the repacking algorithm to do so, but unfortunately its not doing the job. The side chains are not packed properly. Can you help me suggesting on how to go from coarse grained protein to get an all atom model for my protein. Is there any minimization protocol that can take care of this. Kindly let me know.

Thank you.

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