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Interpreting decoy ensemble

Submitted by lah435 on Wed, 2015-06-10 10:25
Category: 
Scoring

When interpreting an ensemble of decoys made with relax or backrub, which structures should be discarded and which ones retained. I get a lot of conflicting advice ranging from “keep them all” to “take the top 10%”. Is there a best practice regarding this?
Also, should the structures be clustered and only the centroids considered?
Any advice would be of help.

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Rosetta 3 - General

auto_setup_metals flag with loop modeling application fails

Submitted by beowulfey on Wed, 2015-06-10 07:44
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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Rosetta 3 - Applications

Resfile as a input for InterfaceAnalyzer

Submitted by palak8669 on Sun, 2015-06-07 21:46
Category: 
Docking

So, I have a pdb complex of a virus and antibody and I wanted to compute the binding energy of the given complex. I know that I need to use InterfaceAnalyzer for this task, but the problem is that the input of the InterfaceAnalyzer application is a resfile. So, how am I supposed to connect these two, the resfile and the pdb file ?

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Rosetta 3 - Applications

How to prepare the pdblist file for docking_ensmble in Rosetta3.4

Submitted by sunlufinal on Mon, 2015-06-01 19:27
Category: 
Docking

Did anyone do ensemble docking using rosetta3.4?
I don't know how to prepare those seemed like energy score(lowres_reference_energies_ , and highres_reference_energies_ from source code) at
the end of pdblist file?

An example of the pdblist is below:

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Rosetta 3 - General

Issues running the Matcher in 3.4 and 3.5

Submitted by Jhreed on Tue, 2015-05-26 11:38
Category: 
Enzyme Design

Hello,

I've run into an issue getting the Matcher to work correctly. I have attached a log file with the error I am receiving (In this particular case I ran 3.4, but the error is the same for 3.5). The specific error is below:

ERROR: olditer != target_restype_index_map_.end()
ERROR:: Exit from: src/protocols/match/downstream/SecondaryMatcherToUpstreamResidue.cc line: 677

Any help would be greatly appreciated and if additional information is needed I would be glad to provide it.

Thanks!

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Rosetta 3 - General

How to use Rosetta to DISCARD a protein-protein docking interface?

Submitted by cossio on Tue, 2015-05-26 06:24
Category: 
Docking

Suppose I have two proteins A and B. I know they bind but I don't know the conformation of the complex. There is a region of interest in the surface of protein A, and I have reasons to believe that A and B DO NOT bind through this region. How can I use Rosetta to DISCARD a docking interface?

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Rosetta 3 - Applications

Ensemble Docking in Rosetta3.5?

Submitted by protos_heis on Fri, 2015-05-22 06:42
Category: 
Docking

I apologize if this has been asked before, but I couldn't seem to find any information on it. Is the EnsembleDock protocol available in Rosetta3.5? I don't see a specific executable for it in the rosetta/source/bin directory. Do I just use -l <pdblist> instead of -s <pdbfile> in the normal docking protocol? And can I still use constraints in EnsembleDock?

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Rosetta 3 - Applications

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