Question: Best Program/Tool/Server To Predict Fold Types/Structural Family For Unannotated Pdb Structures.
2
gravatar for Pals
8.0 years ago by
Pals1.3k
Finland
Pals1.3k wrote:

I am working with large number of proteins. About 80% of those structures have their folds/families/superfamilies classified by CATH and SCOP (I am using CATH). Therefore, I want to predict folds for the remaining 20% of the structures also. I would like to know if there are any prediction tools that can classify those proteins into one of the CATH olds/architecture/superfamily.

Thanks!

Kisun

pdb • 2.8k views
ADD COMMENTlink modified 7.7 years ago by Khader Shameer18k • written 8.0 years ago by Pals1.3k
1

For the 20% that do not have families assigned, do you have structures or sequences only?

ADD REPLYlink written 8.0 years ago by Michael Schubert6.9k

Structure always comes with a sequence :)

ADD REPLYlink written 8.0 years ago by Khader Shameer18k
3
gravatar for Michael Schubert
8.0 years ago by
Cambridge, UK
Michael Schubert6.9k wrote:

Have you looked at HMM-based classification tools?

edit: You can also do a BLAST search with sequences on the CATH database here that gives you the most similar fold.

ADD COMMENTlink modified 8.0 years ago • written 8.0 years ago by Michael Schubert6.9k

Yes, I tried but these programs just assign my protein to one of the available folds/superfamilies from SCOP/CATH/Pfam. In fact I want the prediction programs.

ADD REPLYlink written 8.0 years ago by Pals1.3k
2
gravatar for Jan Kosinski
8.0 years ago by
Jan Kosinski1.6k
Jan Kosinski1.6k wrote:

If you could live with SCOP, you could use fastSCOP: http://fastscop.life.nctu.edu.tw/intro.php

From the website: "fastSCOP is a web server that rapidly identifies the structural domains and determines the evolutionary superfamilies of a query protein structure. This server uses 3D-BLAST to scan quickly a large structural classification database (SCOP1.71 with <95% identity with each other) and the top ten hit domains, which have different superfamily classifications, are obtained from the hit lists. MAMMOTH, a detailed structural alignment tool, is adopted to align these top ten structures to refine domain boundaries and to identify evolutionary superfamilies."

ADD COMMENTlink written 8.0 years ago by Jan Kosinski1.6k
2
gravatar for Khader Shameer
8.0 years ago by
Manhattan, NY
Khader Shameer18k wrote:

"I want to predict folds for the remaining 20% of the structures also."

IMHO, you cannot assign an existing SCOP class to these entries, because these 20% are novel .

It is true that approximately 20% of proteins in PDB is not associated with any known SCOP classification. SCOP curators are well aware of these group of structures. This 20% structures are not assigned a classification due to the sequence-structure diversity of those structures with rest of the members in PDB. For example the structures my contain additional embellishments in structure that will disqualify them from being a member of a particular fold/class. Some of these may get merged into existing classes in the future or depending upon the number of new members with similar features, it may add to a novel fold. As large part of SCOP is manually curate, you may need to wait until SCOP curators assign a fold details to these entries.

ADD COMMENTlink written 8.0 years ago by Khader Shameer18k

Thanks a lot for the insight.

ADD REPLYlink written 8.0 years ago by Pals1.3k
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