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Joined: 04/18/2009
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I couldn't find a thread about this topic yet, so I was wondering if (and how) the new template alignment feature has helped your folding.

Here's the way I used it in puzzle 411:
- The templates were not modified. When accidentally moving amino acids in a template, I reset it.
- The amino acids of the unknown protein were moved to get a "reasonable match" for a template before trying to align it.
- Breaking the unknown into smaller chains seemed to always reduce the score, so, when possible, I tried to build the longest chains of amino acids before aligning the structure.

Attached is the alignment I ultimately used. Sorry I didn't get a picture of the protein itself while the clock was running down.

AttachmentSize
align_411_a.PNG807.93 KB
Joined: 06/17/2010
Easier way to use that tool

when you have chosen one template is "hide" all other in template reserve, then put entire structure in one piece and then cut it in pieces.
When you want to use few of them in partial threading (some part from one template, some from another) the way you show is better.
I take one template and modify it to best fit structures and hydrophobics not exact aas structure.

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