I am interested to obtain protein models for further molecular dynamics studies. I have already used I-Tasser and Robetta servers and in some cases the RMSD values obtained in I-Tasser are too high to validate the models whilst others as Robetta spent entire months to retrieve results.
for this purpose you can use
comparative hology modeling tools are:- as follows
- swiss-model
- Geno3d
ab-initio modeling
you can take I-tasser
if you go for high quality the you take Modeller
I completely agree with Mr. Vinod.
It will be better to go with modeller and follow the tutorial provided by them.
https://www.youtube.com/watch?v=yskL5w20kfQ
Hey Raúl, nice to read you! Just ask to Sergio Enríquez Flores from my Lab. 10840900 x 1142.
In this case you can use HHpred server ((http://toolkit.tuebingen.mpg.de/hhpred).
Vinod, Tarun, Gabriel and Vivek,
Thanks a lot for your valuable suggestions, first I´ll try with Modeller and thereon with the other options!!
Modeller is one of the best software for 3D modeling.. You can also try Robetta
hi Raúl Argüello-García,
Modeller is the best tool for 3D modeling if the homology of your protein with template structure is more than 35 %. If u r unable to find the homolgy template then threading and abinitio calculation of protein modeling is the only choice which u can achieved by using I-tasser and robetta server.
all the best for work :)
Hi Kannan, thanks for your kind attention to my question. In fact my proteins in general have a TM-score >0.5 in I-Tasser but in some cass it is lower hence I should take other options. I´m trying Modeller for these latter cases and I hope it work better...
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