Question: Looking for exercises on protein structure modelling
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gravatar for jachymb
25 days ago by
jachymb0
jachymb0 wrote:

Hello, I am supposed to prepare a tutorial on protein structure modelling in a bioinformatics course. It should include homology modelling / threading exercises. Could you recommend any resources for teaching which would help me create some exercises to illustrate the basic workings of these methods to the students doable on a whiteboard or the computer within say, 1 hour? Thanks!

ADD COMMENTlink modified 25 days ago by Bastien HervĂ©4.0k • written 25 days ago by jachymb0
1

What I personally do when I need to present something I'm not fully confortable with, I first get myself confortable with the subject. You have to get into book, publications, forum, tutorials... If you follow a random tutorial at the first good question (if you have one) you're doomed

If you're already confortable with the subject, try some tutorials (youtube, powerpoint...) and redo & modify parts you found interesting for your course

http://www.bpc.uni-frankfurt.de/guentert/wiki/images/b/b1/180625_Tutorial_Modelling.pdf

ADD REPLYlink written 25 days ago by Bastien Hervé4.0k
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Can you clarify what you mean by exercises? Something interactive for the students to actually do, or just ways of running the software etc?

I guess you will have to break this down in to various concepts. Start with something like sequence alignment (something I've done with undergrads in the past is introduce them to alignment via Phylo (though the link seems to be playing up for me at the time of writing). This will probably also necessitate introducing them to BLAST (if they aren't already familiar).

You'll need to introduce them to concepts such as RMSD minimisation. You can show them how this works with the appropriate functions in UCSF Chimera, so they can get a feel for the process. It's not what I'd call an 'exercise' in threading as such though. Perhaps you can provide them with PDBs of sub-domains of a larger protein and have them fit/superimpose them in an iterative manner?

Just some ideas of the top of my head anyway..

ADD REPLYlink written 25 days ago by jrj.healey11k

Something interactive is much preferred.

ADD REPLYlink written 25 days ago by jachymb0

There are plenty of learning resources available at PDB learn page. If you use ideas/materials in your tutorial then do not forget to provide proper attribution to the sources.

ADD REPLYlink written 25 days ago by genomax65k
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