There are lot of choices available for protein with highest identity and it is really difficult for those having low identity. But still you can use many of them and you have to refine your model according to your need. None of the modeling software gives you the accurate prediction with low identity.
No doubt you will get the better model but its your responsibility to refine it. I would like to suggest you to use either Zhang server (I-TASSER) or MODELLER .
Other choice is you can use MOE, you can edit you sequence according to your need and submit this edited alignment file and build your model with MOE.
Please go through the attached literature where they present the comparison between various homology model algorithm.
Modeller is good option for homology modelling , when query template squence identity is near 30% or above. It gives flexibility in terms of Template selection, Heteroatom inlcusion, loop refinment , model quality assessment.
SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer).
For more information follow this link :
http://swissmodel.expasy.org/
After doing blast if you are not getting any similarity or low seq identity less then 30% then its not possible to use MODELLER then you have to go for any Ab-initio structure prediction method like I-Tasser.
if you have suitable template then only you can go for MODELLER.
Thank You all !!!!
Finally I got a suitable answer of this question:
If sequence identities >40%, almost many servers and packages give similar and satisfactory homology models.
But at lower sequence identities, (25%, are significantly more functional and easier to use when compared with the other homlogy modelling software.
for more info i have also attached the PDF. plz find the attachment
Swiss Model and Phyre2 is best automated homology modeling tool which give all information about predicted model...further u can use InterPro,Protparam,Protscal,QMEAN server,Energy minimization of model etc for refinement and checking model quality.
Modeller is an excellent software for homology modelling when identity of query template sequence is 30% or above. Also MOE is also good and reliable one and also easy to operate.
At lower sequence identities (
Modeller is the best tool for homology modeling. You can also try "Swift Modeller" for easy step of homology modeling. Here is the reference "https://www.ncbi.nlm.nih.gov/pubmed/21258829"
Hi Arvind,
if your protein have low homology you can use phyre2, i-tasser server. Modeller is one of the best software for homology modelling
Gangadhari Vinay Kumar ,
Hi, I my opinion, you can use I-TASSER. When user submits an amino acid sequence, the server first tries to retrieve template proteins of similar folds (or super-secondary structures) from the PDB library by LOMETS, a locally installed meta-threading approach.
In the second step, the continuous fragments excised from the PDB templates are reassembled into full-length models by replica-exchange Monte Carlo simulations with the threading unaligned regions (mainly loops) built by ab initio modeling. In cases where no appropriate template is identified by LOMETS, I-TASSER will build the whole structures by ab initio modeling. The low free-energy states are identified by SPICKER through clustering the simulation decoys.
In the third step, the fragment assembly simulation is performed again starting from the SPICKER cluster centroids, where the spatial restrains collected from both the LOMETS templates and the PDB structures by TM-align are used to guide the simulations. The purpose of the second iteration is to remove the steric clash as well as to refine the global topology of the cluster centroids. The decoys generated in the second simulations are then clustered and the lowest energy structures are selected. The final full-atomic models are obtained by REMO which builds the atomic details from the selected I-TASSER decoys through the optimization of the hydrogen-bonding network
Regards,
Sahar
my question is when i did homology modeling of my target protein and after refinement it shows some result by using Modeller, but when i used Swiss-model server it show better results, so which one is best for homology model prediction.
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