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Show I be using beta_nov16 scorefxn?

Category: 
Scoring

ref2015 is the default at least in pyrosetta and is beta_july15 without the need for the boolean option `correction:beta_july15` to be set.

In the cartesian ddG paper, Park et al. 2016, beta_nov16 is made, which has several difference (below, code used here).

Post Situation: 

params file for beta-amino acids

Category: 
Non-Canonical Peptides

Hi all,

I've been trying to insert a beta-amino acid into peptide, let's say, beta-homo-leucine. It seems that a params file for beta-hLeu is needed. Unforutnately, there is no params file for beta-hLeu in database in Rosetta, and molfile_to_params.py only works for alpha-amino acid. I've also visited https://rosie.rosettacommons.org/documentation/beta_peptide_design, but did't find helpful solution. So my question is:

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Protein Ensemble RosettaLigand Docking

Category: 
Docking

Dear Rosetta Users, 

I have an ensemble of protein conformations obtained by means of MD (Molecular Dynamics) simulation.
I would like to know if a recent protocol is available to dock one ligand to this protein ensemble using RosettaLigand.

 

Thanks in advance.
 

Samuele

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Can rosetta generate a centroid model based on the rna sequence?

Category: 
Structure prediction

For RNA, what kind of model can be defined as a centroid model?

Does rosetta have a function to generate a centroid model for RNA? For proteins, pose_from_sequence(sequence, 'centroid' ) can be used to generate a centroid model from the sequence. Is there a similar function for RNA?

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Atom-wise energy terms from nearest N-neighbors

Category: 
Scoring

Hello PyRosetta users,

Can you please advise me on how I should go about calculating atom-wise energy terms?

Should I simply sum pairwise energies for the nearest N-neighbours or is there a better way of doing this?

 

Thanks!

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Protocol for adding/mutating non-canonical AA

Category: 
Chemically Modified Residues

Hi all,

I have been trying for some time to implement non-canonical AAs into PyRosetta. I have the params file for the residue but when it is passed on via the -extra_res_fa , pyrosetta still won't recognize it. Next to pyrosetta being able to read this AA in a pdb, I also want to mutate (canonical) AA into modified AAs (say hydroxyl group into acrylate). The mutate_residue only takes one character as an argument that corresponds to the canonical AAs, whilst a three letter argument would be preferred. 

Post Situation: 

Protocol for adding/mutating non-canonical AA

Category: 
Chemically Modified Residues

Hi all,

I have been trying for some time to implement non-canonical AAs into PyRosetta. I have the params file for the residue but when it is passed on via the -extra_res_fa , pyrosetta still won't recognize it. Next to pyrosetta being able to read this AA in a pdb, I also want to mutate (canonical) AA into modified AAs (say hydroxyl group into acrylate). The mutate_residue only takes one character as an argument that corresponds to the canonical AAs, whilst a three letter argument would be preferred. 

Post Situation: 

Should I be stripping water molecules from my input structure for Rosetta Design?

Category: 
Design

So I've ran my fixbb rosetta design script and have been happily doing some analysis work, but it just occured to me that I had stripped all the water molecules from my input protein structure and I'm curious whether that biases the rosetta design in a negative way.

What I want to do with my project is to take a fixed-backbone structure of my choosing, optimize the sidechain identities using Rosetta, and then ultimately express it in a cell to see if the optimized sequence folds back into the original backbone conformation.

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