I have some questions regarding homology modelling i.e, how can I find the protein sequence ,which as already has a structure in PDB?
Hi Shivkrishna
Now a days most of the databases are crosslinked...if you know that a protein has a structure in PDB...do a search ce using different parameters....and once you get that file...you should also be able to retrieve the protein sequence....I don't see any major problem here...
There are some very nice homology modeling servers, such as Phyre2.
http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index
Use BLAST, select database as PDB. e.g. go to the following link,
http://blast.ncbi.nlm.nih.gov/Blast.cgi
Then select "protein blast";
Paste your sequence and then change the database to "Protein Data Bank proteins (pdb)";
Click "BLAST" submit button a wait a little bit, you should get what you want
You can enter the structure PDB ID in the PDB web page then it will display the and info about the protein structure, on that page u can download the protein sequence in FASTA format.
My question is how to find the a protein seq is already having pdb id ?
say for example i didnt find the a specfic protein from one organism and found in other organism .if i wanted to submit the protein in pdb i want to search NCBI with that organism. so how to find the sequence which is not yet reported in pdb
download the pdb file and viewing in the molecular visulazation tool
there find the your pdb sequence e.g. RASmol
If your question is, how to find sequence of protein, which is at PDB, go to the page of your protein. e.g. here http://www.rcsb.org/pdb/explore/explore.do?structureId=3MUJ and on left top you have in big 3MUJ and just next to it is Display files or Download files. When you click on any of it, right the first choise is FASTA file with the sequence.
If you mean how to find homologues of deposited sequences in other databases, then simply doqnload the sequence as above and use it as query in BLAST search e.g. at NCBI.
If you want to find out, whether some homologue of your protein has already published structure, there are several ways. You can either look for keywords (like name of your protein) or use your protein as query in BLAST either at NCBI, where you can search against PDB database or at PDB page http://www.rcsb.org/pdb/search/advSearch.do?st=SequenceQuery
If you got the PDB id and want to know what is the fasta sequence,
you can use following link to get the file
http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=1GCC
Just replace 1GCC to your PDB id.
If u have sequence on gene id, u can search in uniprot and customize result to shoe pdb. It will give u links if pdb structure exists, that too in batch mode
To find protein having pdb strucutr ,folllow this steps...paste your seq of protein n blastp search window and then select pdb instead of nr in choose database set option..if your protein has pdb strucure you will gets its id or second way goto uniprot and find link to eiher of structure databases..
If you know the PDB already then i would suggest you to go to RCSB PDB and download file as FASTA sequence. This is the simplest way to get the sequence of your known structure.
The options mentioned above cover many of the strategies available to retrieve the sequence of a protein with experimentally known structure. I would like to contribute a cautionary word. It may happen that even when the PDB file corresponds to a given sequence, some sequence stretches lack coordinates. This is because the experimental technique could not determine them. You may want to identify these parts, if you are doing homology modelling. If you already knew about this, please disregard the comment.
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology