Protein Homology Software

Question

[Raygozak]

Is deepview the best software for modeling a heteromeric protein? what are the alternatives?

thanks

Answer 1

[quentin.delettre]

I think it depends if the protein is homooligomeric or not. This case is the simplest.

Have a look at CAPRI and CASP challenge results.

Answer 2

[João Rodrigues]

The answer you deserve is "No" because your question shows you put 0 effort in researching.. a better posed and better thought question would yield you much nicer answers and probably learn you much more than a simple name.

Nevertheless: MODELLER.

[Raygozak]

i did research and most homology tutorials point to deepview or swissprot.

[João Rodrigues]

Don't take me wrong, but Wikipedia tells you about MODELLER.. and if you follow the link from the homology modelling page to the protein structure prediction software page, then you get all the information you can possibly need. Without even going to pubmed.

Also, you could improve your question by mentioning what kind of protein you want to model and if there are templates, if you have other information, the purpose of the modelling etc. That will help us giving a better answer.

Answer 3

[vijay]

I would suggest Modeller any day for any kind of protein !! It has lots of option that you can tweak and customise as per your needs!!!

[quentin.delettre]

I don't want to troll or something, but i think using one tool to make the job for all cases - without even comparing with other - is something wrong. Rosetta is a serious competitor for example.

[João Rodrigues]

For Homology Modelling?

[quentin.delettre]

Yes. See http://robetta.bakerlab.org/ for homology/ab-initio modelling. There is a package for homology modelling in the rosetta software suite.

Also I-Tasser was ranked first at casp2012 ( http://zhanglab.ccmb.med.umich.edu/I-TASSER/ ).

Casp results of 2012 http://predictioncenter.org/casp10/groups_analysis.cgi?type=server&tbm=on&tbm_hard=on&tbmfm=on&fm=on&submit=Filter . The results are for servers.