If the molecular model of your protein of interest is not available in PDB then you have obtain the sequence of that protein from any sequence databases like NCBI or EMBL or from Uniprot then tried to find a Structural homolog of that protein and then build a Model using Homology Modelling technique and then verify it and then use it for your docking using any program.
Your question tells that you are novice to this field and hence, I will suggest you to use ITASSER for predicting the structure of your interest. In case you do not have an institutional email address (needed for ITASSER registration), I can provide you with my account details.
I hope this will be helpful.
To predict protein structure you can use Prime wizard which is a part of the Maestro software package (Schrodinger, LLC, New York, NY), then you can use the predicted structure for docking using LigPrep and Glide Receptor Grid Generation workflow (Schrödinger, LLC, New York, NY).
A good modelling software for homology structures of proteins could be Modeller (http://salilab.org/modeller/) as it uses structural homologies and constraints for the modelling.
Hello Noha,
The various protein crystal structures of ATP synthase are available on RCSB.org. the gene from which it is derived is atpC. So may be you can refine your search by filtering to organism name. the various sequences of ATP synthase is attached on following link. You can also form homologous protein from it. As per your question, for the docking study of your homologue, validation and active site prediction of the obtained structure is very necessary. Enjoy with your science.
http://www.uniprot.org/uniprot/?query=ATP+synthase+AND+organism%3A%22Mycobacterium+tuberculosis+[1773]%22&sort=score
The only way is homology modelling which you need to check and validate before you dock in. .
You have to built the 3D structure using protein modeling methods. In case you find a crystal with enough identity of sequence/structure you may use homology modeling. If less, other approaches are possible such as threading or ab initio modeling. A list of available tools can be found at www.click2drug.org
Enjoy!
Antoine.
Thanks alot every one im a novice in this field and it seems difficult i will do what you all have suggested and if i find a problem i will ask
thanks again every one
hey guys i got a problem
now i couldnt make modelling because all the programs of modelling need licence and i dont have it
i found the enzyme but in fasta format no pdb how can i convert it to pdb ?
its in the following linke if any one can help i will be grateful for him
http://www.uniprot.org/uniprot/Q5TIK8
thanks alot
use Chem 3D ultra (chem office) also u can use online softwares (auto dock)
http://www.softpedia.com/get/Others/Miscellaneous/Advanced-Protein-Sequence-Converter.shtml (download advance protein sequence convertor using this link)
Hai xml formate is available so u download xml formate and convert to pdb using the software it is available freely(http://www.ecrion.com/LandingPage/XMLtoPDF.aspx?_kk=xml%20pdf%20converter&_kt=b8a303c4-41c7-4927-951f-3494b588de09&gclid=CMPXq9_etbQCFYl66wod4ysA0A)
Hi Noha
In your case you have to build a Homological model for your protein
to make this model you can use "Modeller" which is a freeware and doesn't require a licence
to build this model you will need the sequence which is already in your hand, a template which you can get using web service such as BLAST and a software like I said modeller as a freeware or MOE as you have a licence for it in Assiut Uni as I know
After you build your model you have to validate it using some validation techniques according to the identity percent between your sequence and template and I recommend some molecular dynamics optimization.
For docking you can use Autodock which is a freeware also and doesn't require a licence
Good Luck
Modeller is surely the gold standard for homology modeling, also because you can parameterize a lot the process. Another good and more automatic option is given by swissmodel server which can be called directly from the swisspdbviewer environment. Many other tools do exist, please have a check the complete list of tools at www.click2drug.org.
Regarding Molecular Dynamics of portein models, please have a look at this review/tutorial : Nurisso A, Daina A, Walker RC (2012) A practical introduction to molecular dynamics simulations: applications to homology modeling. Methods Mol Biol 857:137–173. doi: 10.1007/978-1-61779-588-6_6.
Have fun!
Antoine.
Dear Noha,
You can easily predict your protein structure, if you know the sequence for your targeted protein. As you novice in the field I hardly encourage you to use online server and I recommended you to use :(http://www.sbg.bio.ic.ac.uk/servers/phyre2/html/page.cgi?id=index).
Best regards
Maytham
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