[BiO BB] software for protein threading

Dan Bolser dan.bolser at gmail.com
Wed Jun 25 16:05:32 EDT 2008

2008/6/9 Javier Forment Millet <jforment at ibmcp.upv.es>:
> Hi, all...
> We are attempting to do a temptative functional annotation for EST-derived
> partial ORFs which didn't found an annotated similar sequence in BLAST
> searches. Could anyone suggest a software for automated fold recognition by
> threading in local computers?

Hi Javier,

Not sure if this is really helpful or not, but I have been working on
a project called PDBWiki, which maintains an FAQ about protein
structures. Although we haven't covered threading explicitly in the
FAQ, perhaps the answer to the following question is useful for you:

How do I build a homology model?


This would probably be your next step after running a threading
algorithm to obtain a sequence / structure alignment. However, as
Martin pointed out, the first thing to try is probably psi-blast, or a
search against a library of HMMs. This is because sometimes you can
find very reliable alignments between sequences that have very low
sequence identity (and so fail to 'blast').


> Thanks in advance,
> Javier.
> --
> Javier Forment Millet
> Instituto de Biología Celular y Molecular de Plantas (IBMCP) CSIC-UPV
>  Ciudad Politécnica de la Innovación (CPI) Edificio 8 E, Escalera 7 Puerta E
>  Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain
> Tlf.:+34-96-3877858
> FAX: +34-96-3877859
> jforment at ibmcp.upv.es
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