I have a protein sequence which I want to see in 3D. I tried Pymol and Cn3D, but the protein files that they have don't have the sequence which I want to see. I have to predict the protein sequence myself. Does anybody know how to do that?
You could only get reasonable prediction if similar fold or homolog proteins are present in the pdb database. I would suggest Zhang server (I-TASSER) in addition to Phyre2.
http://zhanglab.ccmb.med.umich.edu/I-TASSER/
I want to predict the structure. I only have the protein sequence now. I had someone recommending me phyre2 website and I'm trying it now
You could only get reasonable prediction if similar fold or homolog proteins are present in the pdb database. I would suggest Zhang server (I-TASSER) in addition to Phyre2.
http://zhanglab.ccmb.med.umich.edu/I-TASSER/
I trust with old-school methods: PSI-blast (for finding templates) followed by MODELLER (for building the structure)
I have tried Phyre2 and I-TASSER, which normally take hours and days, respectively. Fast approach is to use PSIPRED and HHpred. For my experience, Phyre2 is still doing the better job, but the results from other programmes are also useful and worthy to take into consideration.
I am trying get hold of a publication or website where many server were compared and found that I-TASSER is better but I cant find it. This was a while ago. Since then Phyre has become Phyre2 and many changes have taken place. Sure some one might have it. I would run on both server and compare the results. You should careful in selecting the results. But it takes few days to get results. Good luck
I like Dario's approach and would add trying a BLASTp against "Protein Data Bank proteins (pdb)" as database and and analyze the resulting Structure of the best matches (Cn3D visualization/comparison with queried sequence)
You could also try one of the META-servers, that aggregate different methods, e.g. https://www.genesilico.pl/meta2/. Once you submit your query you will also get a number of a crude models. They should be further refined once you would like to draw any serious conclusions from the predicted structure.
Does the protein you want to model have any close homologs with resolved structure?
In the end, if you dont have anything to confirm that model either by x-ray crystallography or NMR then its hard to use it further confidently. More the related structures already available better and reliable will be your model. Monday I was in a seminar where the speaker was talking about his work on making new protein in silico and predicting the structure but he agreed that without a crystal structure or NMR its hard to confirm the results. Check out his (David Baker) extraordinary work at http://depts.washington.edu/bakerpg/drupal/. I am excited about the work and not discouraging you in any way.
You can use the bioinformatics toolkit (http://toolkit.tuebingen.mpg.de/sections/tertstruct) to first generate sensitive alignments with HHBlits or find templates with HHPred that will be pipelined into a Modeller Prediction Framework.
Have a look at the resources available at the Protein Model Portal http://www.proteinmodelportal.org/ including those accessible in its Quality Estimation Link. Also try http://www.reading.ac.uk/bioinf/IntFOLD/
alright! thanks everyone for the help. I've been using Phyre2 for the moment and it works fine for me. But thanks for the other suggestions :)
Hi, in addtion to above, you can opt for Expasy online server (Automated mode of protein homology modelling), Consurf is also useful.
hi Liyana you can try these following for protein structure prediction
>mode base
>hhpred
>swiss beta model
>mode web
>swiss model
If you have a have a good template, your best option will be: http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index
If not: http://zhanglab.ccmb.med.umich.edu/QUARK/
I-Tasser is a good option too, it was ranked as the number one in the last CAPRI round.
Good Luck!!!!!
Robetta by David Baker's lab is very good for proteins with low sequence similarity/ no templates...I-TASSER is good in case of proteins with good templates
The lastest best methods in CASP-7 bechmarks are: I-TASSER and ROBETTA
http://zhanglab.ccmb.med.umich.edu/I-TASSER/
http://robetta.bakerlab.org/
Hi,
To predict or model the protein structure you can try modeller, then online servers like phyre2, swissmodel, robetta,etc
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