Question: Fold Assignment
3
gravatar for pixie@bioinfo
8.4 years ago by
pixie@bioinfo1.3k
pixie@bioinfo1.3k wrote:

I am trying to assign fold to a particular domain of a protein. Using the FATCAT server, I found that the fold is similar to the OB fold family ( more precisely SSB proteins). I read many journals on this OB fold and found that there is little or no sequence homology among the members of this family. I confirmed this by performing structure-based sequence alignment between my domain and members of the SSB family.

Any ideas regarding what else could be done to will be really helpful...

domain protein homology • 2.0k views
ADD COMMENTlink modified 8.4 years ago by Bilouweb1.1k • written 8.4 years ago by pixie@bioinfo1.3k
4
gravatar for Rm
8.4 years ago by
Rm7.8k
Danville, PA
Rm7.8k wrote:

Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments.

Try
PHYRE Protein Homology/analogY Recognition Engine Protein Fold Recognition Server

DescFold(Descriptor-based Fold Recognition System)

or Pcons-meta server

Consensus Fold Recognition Methods [PPT]

Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains

Also I remember a old Perl program called "Divide-and-BLAST"

ADD COMMENTlink modified 8.4 years ago • written 8.4 years ago by Rm7.8k

thanx so much..

ADD REPLYlink written 8.4 years ago by pixie@bioinfo1.3k
3
gravatar for Neilfws
8.4 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

As suggested in the first answer, it is always good to throw a range of fold prediction methods at your sequence. Some may perform better than others and some confidence is gained if several methods give comparable results.

However, for an uncharacterised protein, often prediction can only take you so far. As you mentioned, the OB fold is common to many proteins: here's the SCOP fold entry and the SSB family entry. Fold/domain information can be useful but sometimes, you just can't go any further with computational analysis and it's time for the experimentalists to up their game and generate more data!

ADD COMMENTlink written 8.4 years ago by Neilfws48k
1
gravatar for Bilouweb
8.4 years ago by
Bilouweb1.1k
Saclay, France
Bilouweb1.1k wrote:

Phyre has a great web interface with many options to visualize data.

If you want to try some other methods for protein fold prediction, visit the web site of the CASP competition. You will find many useful tools (perhaps too much).

ADD COMMENTlink written 8.4 years ago by Bilouweb1.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 755 users visited in the last hour