Hi all,
I'm doing a de novo protein structure prediction using https://zhanglab.ccmb.med.umich.edu
There are two modes for the prediction. QUARK for less than 200 AA and I-TARSSER for bigger proteins. My amino acid sequence is 154 long and my question is will I have the same result if I use both mode? Because the run take a long time, I have't tried it myself.
I've done one QUARK run and the result showed 10 predicted models. Which one is the most reliable result from the prediction? I got a TM score "Estimated TM-score of Model 1: 0.2881 ±0.0833
Estimated TM-score of the Best of Top 10 Model: 0.3309 ±0.0764 " but I don't know how to annotate the result.
Later I will do another prediction, for the same protein but with several changes in the amino acid sequence.If like my first run, I will have another 10 predicted models after the run. If my aim is to compare whether the predicted structure is different between the two sequences, how do I choose the model for comparison and which software or website is recommended for this task?
Thanks!
Hi,
QUARK and ITASSER both are different in many aspects. ITASSER predicts structure on fold based homology i.e. it models protein based upon certain templates.
QUARK is for ab initio protein folding and protein structure prediction. No templates are required for prediction protein structure. It is suitable for prediction of 3D structure of proteins which does not have homologus templates.
So selection of modelling server should be based upon your requirement.
I would suggest you to check whether your protein has any structural homologs by using PDB BLAST.
Then proceed for selection of desired approach for modelling. Apart from these two approaches there is a much famous structure based homology modeling approach. You can SWISS-MODEL, phyre2, A standalone tool- Modeller, RaphtorX for performing structure based homology modeling..
Hi Pankaj,
Thanks for the reply! My one is a virus protein. Usually for this kind of protein, cannot find homologs template right?
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