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General Category >> Help and How-to >> How to create a *.PDB file from a *.FASTA or *.ALN files? https://forum.ugene.net/forum/YaBB.pl?num=1267197515 Message started by Bruno Fantinatti on Feb 26th, 2010 at 10:18pm |
Title: How to create a *.PDB file from a *.FASTA or *.ALN files? Post by Bruno Fantinatti on Feb 26th, 2010 at 10:18pm
Hi!
I need to know how to create a *.PDB file to see the tridimensional structure of a pritein? Thank You! :D |
Title: Re: How to create a *.PDB file from a *.FASTA or *.ALN files? Post by Mikhail Fursov on Feb 26th, 2010 at 10:44pm
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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