I have a crystal structure that has 3 missing amino acids in its loop site, How can I add the missing amino acid to the structure to remodel it.
You can use either Discovery Studio or Modeller for the purpose.
In Modeller use the same structure as template and same sequence as target but make alignment like below.
i.e. your structure sequence.
ABCDEFGHIMNOP ---JKL the missing residue
Prepare alignment like below
>P1;
target headers
ABCDEFGHIJKLMNOP*
>P1;
template headers
ABCDEFGHI---MNOP*
Modeller will model the missing residue for you by using such alignment.
Wishes.
there is an online tool called ModLoop
http://modbase.compbio.ucsf.edu/modloop/
it seems to use the same algorithms as Modeller but it is easier to use
I wonder why you want to remodel? Flexible loops are not always seen in crystal structure.
Be careful before you go for homology modeliing. Flexible loops are often disordered in nature. And modeling such disordered regions is a risky business and affects the reliability of your model. I would suggest first you check the disordered nature of your protein using DisProt or PrDOS and then can try ab initio modeling using Phyre2 tool
Thanks for all comments,
Exactly I face with this problem, because of this, I want to remodel the missing part at my template before homology modelling .
And generally I employ Rosetta software to remodel my loops.
I preform using automated Swiss model to model my target .
Please let me know your idea about this server?
You can try using I-TASSER for modeling. There is no need to reconstruct the loop beforehand, all you will need is the sequence. The performance of I-TASSER for structure prediction is very good (see below for results from the CASP contest for protein structure prediction)
http://zhanglab.ccmb.med.umich.edu/I-TASSER/
Surface loops are generally disordered and internal loops are disordered some times in crystal structures. I still didn't get the rationale behind trying model three residues. Anyways, you have some great suggestions here. Good luck.
Dear Yogesha,
Yes you are right ,But when I Model my target with missing amino acid template(i.e., done in Swiss-model), I face with a problem in helical part, because my target is GPCR .
But this I-TASSER server is very slow. I uploaded my project almost 10 hours ago , but I did not get results.So I downloaded the I-TASSER packet to do it manual.
I have not tried it manually but it takes 1-2 days and even more on web server. The server will build the model well if it finds a template.
Hello.
MODELLER has a loop modeler function that can help you to model the missing residues.
Best regards,
Ricardo Ferreira
Hi,
I use Coot software http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot-download.html and it is quite intuitive. It has a"Fit loop" tool that is quite handy to model loops, especially if you have ED around it. It also allows you to freely build molecules with the "add residue here" button, where you can just add residue and bind them together with at auto refinement tool.
Good luck!
For convenience you can use SPDBV to add missing residues to the protein structure. Also I-Tasser can be employed.
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