December 14th, 2007


Molecular Modeling Programs

Hey all! This is less of a "lab gripe" than a "this is getting frustrating" topic. Although as I am typing this now, someone's timer has been going off for three and a half minutes, which is getting to be "gripe-y". I'm wondering if anyone is intimately familiar with VMD or WebLab modeling programs. I used to be a champion VMD-er, but a few years went by and now I'm pretty rusty. I'd like to be able to superimpose structures upon one another to compare how they line up with binding sites in a complex (ie: in a complex of A1-B1-C1-D1, I would like to see how B2 lines up in the complex in place of B1).

Specifically (in a vaguely specific sort of way), I'm identifying binding sites and comparisons in a G-protein complex containing a G-beta subunit, an RGS protein, a GGL (G-gamma like) domain, a DHEX domain, and a DEP domain. I've got a crystal structure with particular versions of all of these together (and crystal structures have been solved for most of the different G-betas, DEP domains, RGS domains, etc -- just not in complex together -- except for this one I've got my dirty little hands on). I'd like to be able to chop out the G-beta in this crystal structure complex (ie: turn off visual representation of the residues that represent that chunk) and sort of substitute another G-beta to see if it fits the same way (and similarly for the other domains). So to do that, I need to be able to turn off representation of a chunk of this complex (or alternatively, only turn on a particular part) and I need to be able to visualize two sets of pdb codes on one screen. I'd also like to be able to look at the different versions of these pieces next to each other (ie: structurally, what are the differences between RGS 6, 7, 9 etc), which requires the same sort of techniques.

I don't even know if this is possible with VMD or with WebLab, or any other modeling program for that matter. This could all just be a great biochemistry pipe dream. I like WebLab for the list of residues you can pull up in an adjacent window, but I think VMD has many more options for visualization. And more fun toys. And I've only got those two programs because they're free... and I'm not too familiar with any others.

So, does anyone know how to do this, or have a more useful program to use?

On a side note, I am leaving for a bit for the holidays next week, and I can't seem to focus on anything except the page-long (and growing) list of stuff to take care of before I leave... mostly non-lab related. And I can't seem to find the motivation to study for my last final, to do any sort of laundry or house-cleaning attempt, or to start this pile of transfections/IPs/westerns that *probably* should be done before I leave. All I want to do is bake christmas cookies and watch holiday specials on TV. Anyone else feel the holiday motivation drain?
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