I have a protein, but one of its loop has be modeled as similar to a template protein. How can i proceed with this?
For this also you need to have a Prime module of Schrodinger software to refine modelled loop, it will give you the number of loops, you need to select the energetically stable loop for your final HM.
Kiran Lokhande thankyou! is there any other alternatives other than this?
Yes. You can use an online server as well to model loop.
https://modbase.compbio.ucsf.edu/modloop/
Article: Yasaman Karami, Julien Rey, Guillaume Postic, Samuel Murail, Pierre Tufféry, Sjoerd J de Vries, DaReUS-Loop: a web server to model multiple loops in homology models, Nucleic Acids Research, Volume 47, Issue W1, 02 July 2019, Pages W423–W428, https://doi.org/10.1093/nar/gkz403
You can use Modeller as well to build and refine your loops. The loop building and refinement scripts are in built in the software package and you just have to edit them as per your particular system.
You can build loop between two atomic coordinates using spdbv software.
menubar- build> build loop> select two coordinates of your target amino acids.
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