[BiO BB] software for protein threading

Javier Forment Millet jforment at ibmcp.upv.es
Thu Jun 26 06:13:23 EDT 2008


Hi,... I've run iprscan and, of course, it allows functional annotation for some
orphan proteins. Now, the next step is trying to do threading with the rest of
orphan sequences. I'm not interested in building an structure model for these
proteins. I just want to be able to identify a putative CATH/SCOP folding for
them, so that we can do a temptative functional annotation based on the
predicted/confirmed function for that folding.

I've found programs such as threader, prospect, frost, analyst, raptor, tasser,
forte, modeller, SP4, etc. But I have no experience with them (and even don't
know if some of them could be useful for what we want), so I would like to get
feedback from people having used them...

Cheers,

Javier.


> 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?
>
> http://pdbwiki.org/index.php/PDB_FAQ#Q:_How_do_I_build_a_homology_model.3F
>
>
> 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').
>
>
> Cheers,
> Dan.
>
>
> > 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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> >
>
> --
> PDBWiki - http://PDBWiki.Org
>
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>


-- 
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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