You can only look at the 3D structure of a protein if it has been solved. Input your sequence to this website http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/sequence/ to see if the structure of this sequence, or similar ones has been solved. Structures can be viewed using several viewers both online (eg jmol) or stand alone (eg pymol).
Dear Sevan
As matthew said, you can explore for pdb structures of this sequence using related websites. If there is no pdb for your sequence the only way to predict the structure of protein is homology modelling. for more information see also :
http://salilab.org/modeller/
Exists also the SIFTS database developed at EBI http://www.ebi.ac.uk/pdbe/docs/sifts/methodology.html that crosslink together protein sequences with protein structures or with the most similar. Otherwise my advice, if you cannot find your sequence there, is to use an homology modelling tool like the one proposed by Hamed. The only problem in using homology modelling is that you have to have a template structure to use for the modelling. Otherwise exists a lot of methods that predict the structure ab-initio (without any assumption of existence of a template) like FINDSITE or better if you use ROBETTA from baker's lab (http://robetta.bakerlab.org/).
I normally use uniprot or ncbi to see what is known. You may also look at the pdb database. You just need to know the name of the protein to which the sequence belongs. It gives all kinds of pbd's if known. If you need anymore help you can always contact me through my personal mail: [email protected]. good luck
It is depends, which structure you one visualized, if you only want to see secondary structure you can use for example sopma, sas etc, for 3d modelling you can rely on 3d structure of homologous aa sequence if it are available. Here you have link for different tools, which you can use for both purpose http://www.expasy.org/.
Indeed it is important to know what type of structure you want to visualize. However, most visualization tools like pymol and king have a plural of options by which you can see secondary structures as well as 3d structures.
Do a blast search against the PDB database to see if you have a related solved structure. You may also use the server MSAT (http://imed.med.ucm.es/Tools/msat.html). It will find the 3D structure or model one for you.
Thank you so much Dear Pedro. I appreciate that it is is really helpful this above website I have found this
Do pdb blast of the sequence and search for the top aligned proteins with structure at pdb database. PDB is protein databank, the 4 letter code is the structure of the protein with highest identity to your query sequence. if identity is 100-95 pc then its yours sequence's protein structure
cheers
Can any one tell how to edit FASTA header format like the one below:
I wanna change for example
>schistosoma_mansoni_prjea36577|Smp_070930
to
>Smp_070930.1 or
>Smp_070930.2 etc
I will have to do this for large number of proteins identified in a fasta format.
Thanks.
Do you mean you are looking for it to be done automatically? You could open your FASTA file in notepad. Also, a text editor likemSublime allows you to do a bit more (e.g 'replace all/with'. Another good one is MEGA (now in edition X) converts between files and is very user friends it's main purpose is sequence and analysis of different sorts. If these don't suit your needs, you may have to write a script of your own and run it.
Cheers & Good Luck!
Hello
The sequence is available in NCBI
You can search here
https://www.ncbi.nlm.nih.gov/protein
Here u can find the 3D structure of ur protein
https://www.rcsb.org/
If the 3D structure is not available you can predict 3D Structure here
I-TASSER server
(CASTp, Autodock vina, Swissmodel, Qsite, Chimera, RasMol or JMOL, MOE, BIOVIA Discovery Studio) show the cavity ...
Good Luck.
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