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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

Should I trust the score output from relax used with a protein complex?

Submitted by cossio on Thu, 2015-05-07 06:08
Category: 
Scoring

I am using the relax.linuxgccrelease application to relax a protein complex. I simply send the pdb containing all of the fomed complex to relax.

The score outputted by relax represents the sum of the score of folding plus complex formation (in Rosetta arbitrary units, of course)?

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Rosetta 3 - Applications

scorefunction Talaris2013

Submitted by dave on Tue, 2015-03-03 02:13
Category: 
Scoring

Hi,

I'd like to use new scorefunction from article by O'Meara et al., 2015, from JCTC. Acording to supplementary info the published ElecHBv2 is the Talaris2013. There is missing line 'yhh_planarity 0.5' in my installation (in comparison with published article). Should I add this line or is it set there by default? what does this line mean.

thanks,
David

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Rosetta 3 - General

Reproduce Robetta's ddg values of interface alanine scan using Rosetta?

Submitted by cossio on Mon, 2015-01-19 07:14
Category: 
Docking
Scoring

Is there a protocol on Rosetta to obtain Robetta's (http://robetta.bakerlab.org/) ddg's calculations of interface alanine scan functionality?
I don't care if they use an older version of Rosetta. I just want to obtain ddg's values that are as close as possible to those returned by Robetta. What protocol do they use?

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Rosetta 3 - Applications

Different scoring applications (score vs score_aln vs score_jd2, etc.)?

Submitted by cossio on Fri, 2014-12-26 07:19
Category: 
Scoring

What's the difference between the different scoring applications?

In my bin folder I find the following scoring applications:

score, score_aln, score_aln2, score_jd2.

What's the difference between them?

(I am omitting the trailing .default.linuxgccrelease, or mpi.linuxgccrelease, since I know those denote parallel vs non-parallel versions)

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Rosetta 3 - Applications

Combine flags file with command line arguments?

Submitted by cossio on Mon, 2014-12-22 13:52
Category: 
Compilation
Structure prediction
Docking
Design
Scoring
Enzyme Design
Loop Modeling
Constraints
Symmetry
Small Molecules
Chemically Modified Residues
Fragment Generation
Membrane
Non-Canonical Peptides
Nucleic Acids
Phenix / MR Rosetta

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list

Thanks.

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Rosetta 3 - General

Change in binding energy after mutation in interface?

Submitted by cossio on Mon, 2014-12-01 06:27
Category: 
Scoring

I have the .pdb structure of a complex of two chains.
I want to try the effect of a mutation in one of the interfaces on the binding energy. I am new to Rosetta. Can someone explain step by step how to compute this delta-delta-G?
Thanks.

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Rosetta 3 - General

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