Question: Availability of homology model
0
gravatar for joepiwity
3.6 years ago by
joepiwity0
Pakistan
joepiwity0 wrote:

I intent to construct structure of protein by homology modeling. How would I know if previous homology model of my protein is available or not without going into extensive search results?
 

ADD COMMENTlink modified 3.6 years ago by Elisabeth Gasteiger1.6k • written 3.6 years ago by joepiwity0
1
gravatar for Ibrahim Tanyalcin
3.6 years ago by
Belgium
Ibrahim Tanyalcin940 wrote:

Dear,

Homology modeling will try to model the regions of your protein that are similar in sequence to other proteins of known structure  in a given database. It is possible that certain regions of your protein will not be modeled. That being said you can check at:

http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi

if your protein is not there try using http://swissmodel.expasy.org/  This tool will get your query protein sequence and try to find templates that exist in their database.

There are also other automated servers such as I-TASSER: http://zhanglab.ccmb.med.umich.edu/I-TASSER/

You can either use native I-TASSER algorithm which takes into account existing templates or the QUARK: http://zhanglab.ccmb.med.umich.edu/QUARK/ which does ab initio prediction, meaning from scratch, without templates and only taking into account the amino acid sequence.

You can also try the automated PHYRE2 server: http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index 

Here you will have 2 modes, normal and intensive. Templates are used here as well. For all residues you will get a key of confidence scores giving you an idea about the reliability of the model/region that is modeled.

All these are some guidelines. The aforementioned websites will send you results within 1-4 days, no additional work needed other than submitting your fasta sequence. The resulting models should be interpreted carefully, trying to take into account proteins with similar function/structure with known 3D confimation where possible,

I hope this helps,

Good luck with your research,

ADD COMMENTlink written 3.6 years ago by Ibrahim Tanyalcin940
1
gravatar for Elisabeth Gasteiger
3.6 years ago by
Geneva
Elisabeth Gasteiger1.6k wrote:

Further to Ibrahim's reply:

If your protein sequence is in UniProtKB, you can have a look at the "Structure" section of the entry, which links to various model databases, even if no cross-references to PDB are available, e.g. ProteinModelPortal, SMR (Swiss-Model repository), ModBase and MobiDB, e.g. http://www.uniprot.org/uniprot/Q96J66#structure

ADD COMMENTlink written 3.6 years ago by Elisabeth Gasteiger1.6k
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