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How to create a *.PDB file from a *.FASTA or *.ALN files? (Read 11593 times)
Feb 26th, 2010 at 10:18pm

Bruno Fantinatti   Offline
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Brazil

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Hi!
I need to know how to create a *.PDB file to see the tridimensional structure of a pritein?
Thank You! Cheesy
 
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Reply #1 - Feb 26th, 2010 at 10:44pm

Mikhail Fursov   Offline
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Hi!

You can't create detailed PDB-like 3D structure from just a sequence or alignment. This task is a big challenge for a lot of researchers today and there are no reliable solution still.

You have 2 options with UGENE:

1) If you know the protein/family encoded in you FASTA or ALN file you can use the protein name to fetch the 3D structure from PBD database. Just use File->Access remote database menu, select PDB and type in the name.

2) Use secondary structure prediction methods available in UGENE (GOR/PSIPRED) to locate certain secondary structure regions in the sequence. But it won't give you 3D image.
 

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