Hi, I have a question regarding modeling the loop of an already determined structure of a protein de novo. I want to change the entire sequence of the loop regions of the protein with random sequences and also I want to extend the length of the loops in the protein structure. I have searched through a lot of papers but I am not able to find any specific paper about such an approach.. So, I want to know can Modeller help in solving this problem and also I will be highly obliged if anybody can refer me to some good paper on De novo loop modeling .. Looking forward for a positive and fast reply,.....
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
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South Korea
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On 12 January 2011 06:04, bharat lal monu46010@yahoo.com wrote:
> Hi, > > I have a question regarding modeling the loop of an already determined > structure of a protein *de novo. *I want to change the entire sequence of > the loop regions of the protein with random sequences and also I want to > extend the length of the loops in the protein structure. I have searched > through a lot of papers but I am not able to find any specific paper about > such an approach.. So, I want to know can Modeller help in solving this > problem and also I will be highly obliged if anybody can refer me to some > good paper on De novo loop modeling .. > > 1. Remove the loop region form your template. 2. Align the resulting template sequence with the same sequence but include the desired aa sequence. The alignment shoud look like this:
>template AGF--------GHK >target AGFRRKTYDERLGHK
where RRKTYDERL is the sequence of the loop you want to model.
3. The use loopmodel build a new model and the loop conformation ab initio as in this example:
http://www.salilab.org/modeller/manual/node32.html
homology models will be named as "target.B9999*.pdb" whereas loop models "target.BL999*.pdb"
4. Create as much as possible loopmodels by setting the following parameters accordingly:
a.loop.starting_model a.loop.ending_model
Also bear in mind that loop modeling works well for loop <12 aa. When the length exceed ~15 aa the reliability drops abruptly. I would recommend searching the mailing list about loop modeling, this subject has been covered extensively in the past.
Thomas
PS: QUARK ab initio server has a new option that allows distance restraints. The problem is that it has a 200 aa limit and you have to include the surrounding environment of the loop in order to get an accurate prediction. I intend to try this option soon, so I'll keep you posted.
First of all try to post to the same thread. There are people like you who might seek the same information and will find it helpful.
> > I tried following ur procedure but I am getting the following error :- > > "Sequence Difference between alignment and pdb residues" > > What I did is, I deleted the sequence of loop from the pdb file also .. > Now its giving the error "No. of residues in the alignment and the pdb file > are different" > >
You might find this helpful:
http://www.salilab.org/modeller/FAQ.html#17
Look at you .pdb and .log files and THINK. I model missing loops all the time.
I have a doubt regarding this procedure , since the sequence of loop present > in the target doesnot match with that of template , then how the structure > will be modelled ?? ... As Homology modeling relies completely on copying > the backbone of template sequence and then model the structure accordingly > for the target ... > >
Loop modeling is designed for cases where you have not template - it wont use any information from .pdb files. I asked you something last time, to search the mailing list as this question has been answered in the past. Just before your post someone asked about loop refinement and I posted a link to the manual (in fact you could find that section of the Manual by yourself if you had searched properly) which describes the loop modeling method:
http://www.salilab.org/modeller/manual/node452.html#SECTION:loopmethod
loopmodel.loop.md_level controls the refinement level, I recommend setting it to refine.very_slow and create as much loop models as possible. The refinement procedure encompasses MD with Simulated Annealing.
Next time search the mailing list and the manual thoroughly before you ask something that has been answered before.
Thomas
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bharat lal -
Thomas Evangelidis