[modeller_usage] Loop Modeling in a Protein-DNA Complex
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Subject: [modeller_usage] Loop Modeling in a Protein-DNA Complex
From: Alexander Predeus <>
Date: Fri, 16 Mar 2012 00:33:45 -0400
Hello all,
I'm trying to fill the gaps in a protein-DNA complex of a moderate size (~ 15k heavy atoms). There are two protein chains with 13 missing pieces overall, most are 2 to 8 AA, but two are fairly long (~ 15 AA). I'm modeling ONLY the missing parts for I don't want the X-ray structure perturbed, and I included DNA molecule as a ligand (with HETATM identifier and "." in alignment).
From reading this mailing list, I've realized that it's better to generate a lot of models using a faster routine (e.g. refine.very_fast) and then take the best one, rather than do longer refinement and generate less models.
The question I wanted to ask, is what is the best assess method I can use, considering the nature of my task? I'm using DOPE right now, but in the manual I've also seen mentioning of DOPE-HR. Would it slow down the loop refinement process a lot (or at all)?