Ligand in standalone version

Case number:699969-991900
Topic:General
Opened by:limfoldit
Status:Open
Type:Question
Opened on:Saturday, February 18, 2012 - 09:05
Last modified:Tuesday, February 21, 2012 - 19:08

Firstly, congrats on the Eiben et al. 2012 Nature paper.

It's inspired me to try a somewhat similar approach but using the standalone version. I figured I'll try it out first, before putting it online as a puzzle.

I'm trying to model the effects of altering an active-site residue, and also find out what other changes could accommodate alterations at that particular residue.

However, my structure has a ligand in it. Is there a way for me to display the pdb file with ligand(hetatom) in the standalone version? Or is that something that's still in the works?

Thanks.

(Sat, 02/18/2012 - 09:05  |  1 comment)


rmoretti's picture
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In order for Foldit/Rosetta to know how to work with residues/ligands, it needs to have a "params" file to describe the residue chemically (how it's bonded, which bonds can rotate, etc.) in addition to the PDB coordinates. Foldit by default comes with such params files for the standard residues, and for puzzles like Eiben et al.'s Diels Alderase ones, the params file for the special ligand were provided with the puzzle information download.

If you're using the standalone version with a ligand, you'll need to generate and load the params file for that ligand in order for Foldit to work with it. Rosetta itself comes with scripts to generate the requisite files (how to do so is in the documentation for the ligand docking application), but I don't know if the standalone Foldit program comes with such a script.

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