I would like to model three missing loops in a protein. Unfortunately, there is no similar protein having these missing residues (template is not available). I tried to use FALC-Loop server, but it seems the website is not working. Could anyone suggest a server or software to add these loops?
You can use coot to build your loop (missing residues/atoms) and refine them.
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
Thanks Priyanka and Dr. Chaturvedi for quick replies. :)
For the time being I am trying to model the loops in modeller.
I'll also look into the modloop and coot as suggested by you.
modloop and modeller is the same things! Just modloop is the server.
Coot is a good alternative. You also have FREAD (you have an option for membrane protein if needed)
But my opinion is go for Modeller, where you can customise as you which.
Trust it help!
http://opig.stats.ox.ac.uk/webapps/fread/php/
Try Rosie , the web server of Rosetta software. It is really easy to use, good documented and quite fast! http://rosie.rosettacommons.org/
you can use RAPPER protein modeling server. plz use link mordred.bioc.cam.ac.uk/~rapper/
If you have the access to Schrodinger software suite, then it has a Prime and PrimeX modules. They are very good in modelling the reliable loop confirmations and they have the option for energy minimization after modelling them.
If you dont have the option, then you can use the Modloop server or use the model-loop.py or loop.py scripts of the modeller software. Even FREAD server (Mentioned already by Aurore) is also a very good server for loop modelling
There are number of ways, I'm trying to summarize, hope it helps.
ModLoop/Modeler is trustworthy as Sali lab runs the program for longtime (First server to help people modeling).
COOT is a good alternative, but works better when you have the electron density files.
Schrodinger if available to you, would be good alternative.
Discovery studio (if available), follow the following tutorial, http://accelrys.com/resource-center/case-studies/pdf/antibody_modeling_app_guide.pdf
MOE (if available) could also be helpful, http://www.bioinfo.rpi.edu/bystrc/courses/biol4550/homework4.pdf
If the loops are extremely important for your work, you could also go for ab-initio modeling. In that case, following would be helpful.
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.23.5586&rep=rep1&type=pdf
Yuo can download the modelling program WHAT IF. That will "fill gaps" and help you to model loops.
FALC is rather good server for loop structure prediction, it can deal with long loops up to 50 aa
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