My protein structure is not present in PDB and I have to compare the structure of my protein with best fit. How can I proceed?
I don't even have the basics and I am quite worried about this, as I have to do this and I am finding this quite unclear when I go through the books. If it is possible, please elaborate your suggestions.
Thank you.
Hey Prem,
have you looked at the SWISS PDB Modeling Tutorial? It explains the basics of molecular modeling.
Hope that helps you.
Maybe others have better suggestions
-Ijad
http://spdbv.vital-it.ch/TheMolecularLevel/SPVTut/
Hey Prem,
have you looked at the SWISS PDB Modeling Tutorial? It explains the basics of molecular modeling.
Hope that helps you.
Maybe others have better suggestions
-Ijad
http://spdbv.vital-it.ch/TheMolecularLevel/SPVTut/
as lijad sayed you can use Swiss modeller, an automated online resource for protein modeling. either use can use your own template by doing BLAST of your sequence using PDB Databank as your reference Database and one with showing most identity with your sequence is your template for modeling or go for random. other online resource are also available which you can use.
You can model the structure of your protein by using swissmodel tool in expasy tools....
can I proceed by following the tutorial (http://spdbv.vital-it.ch/TheMolecularLevel/SPVTut/) as suggested by Mr. Ijad ?
Prem, you can do very simply using Swiss modeller, automated version. You have to log in there or register there and create a workspace and then using the automated mode, you just need to provide the protein sequence, and the rest will be done by the software itself. its free and very simple. u can do it !!! :)
Hi Prem,
First, it is not clear for me, what do you want to do? and what data do you have?
"My protein structure is not present in PDB. and I have to compare the structure of my protein with best fit"
You want to derive a 3D model of a protein?
If so, you don't have a template?
If so,this is so called "difficult case modeling" and it is not a task for a beginner. Yet you can always try.
If I were you: first:, some basic reading about homology modeling (Swiss and Modeller) and then you will get some idea about this mattery.
It is a really bad thing to play with homology modeling without knowing what are you doing. You can always try automotaed homology modeling with Swiss but still: will you know what are you doing?
good luck
I think you can try either with swiss or other websites just by submitting the primary sequence of your protein.
Results will tell by themselves the consistancy of the model simply by comparing the phylogenic distance between your protein and the template proposed by the webservers.
The closer they are the best the model will.
Some adresses (without any registration):
I TASSER by zhang Lab (best ranked at the last CASP) :http://zhanglab.ccmb.med.umich.edu/I-TASSER/
Phre2 (very friendly interface): http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index
enjoy ;)
Check these two papers:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012483
http://www.cicy.mx/Sitios/Journal/pdf/2011/October/HighDefinition/IBCJ_2011_1_1_26S.pdf
If you have little experience the second one can be particularly helpfull.
There is a community experiment named CASP, which determines what is the best server/software to predict the secondary/tertiary structure of a protein. So far (and by far) I-TASSER has been ranked as the best tool to do such predictions. I highly recommend you to use it. Here is the link.
http://zhanglab.ccmb.med.umich.edu/I-TASSER/
There is also MODELLER from Sali's lab, which one of the best software to that.
You could try the tutorial, if you are not afraid of a bit of scripting (python):
http://www.salilab.org/modeller/tutorial/basic.html
But maybe your protein has already been modelled? It worth having a look on the Protein Model Portal (PMP):
http://www.proteinmodelportal.org/
http://www.proteinmodelportal.org/?pid=advancedQuery
You can also use CPH server for modelling..n u can also refine ur modeled structure through MODrefiner
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