Questions tagged [rosetta]

Rosetta and pyrosetta are a computational biochemistry toolkit that enables a variety of force-field based calculations ranging from binding scores to missing loop addition and enzyme design.

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Define and calculate pep_sc and pep_sc_noref in pyrosetta

I can calculate total rosetta energy score of a peptide-protein complex. However, when using flexpepdock module from pyrosetta I didn't find anything direct parameter like pep_sc or pep_sc_noref in ...
Shafayet Rahat's user avatar
1 vote
1 answer

How to calculate various properties of a protein structure per atom using PDB2PQR and Rosetta tools (or any other tools)?

Currently, I am implementing a descriptor of protein structure and would like to calculate properties per atoms like charges, hydrophobicity, hydrogen bond donors / acceptors, hydrophobicity, ...
Nurlybek Amangeldiuly's user avatar
2 votes
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How are different forcefields developed/evaluated?

The Rosetta software can use a variety of different energy functions: Ref2015 GenPot Beta-Nov16 How are these energy functions developed and validated? Is it common to do a single protein design ...
Seanny123's user avatar
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How to specify input resfile for Rosetta?

I'm trying to run the following Rosetta command. ...
Seanny123's user avatar
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3 votes
1 answer

How many models should be generated by rosetta for denovo protein structure prediction?

How many models should be generated by rosetta for de novo protein structure prediction of a 382 long sequence? In the tutorial, it says 50,000 models but practically it takes a lot of time (weeks) to ...
DanielSebas's user avatar