I am interested to find out if there is a way to get protein data bank (PDB) co-ordinates from a FASTA format based query. The problem briefly is this: If I search for an enzyme from the glycolysis pathway, say in C. elegans on PDB, I am repeatedly getting the same annotated molecule but nothing in regards to C. elegans. I need some help with regard to getting a PDB format from my FASTA format input.
http://www.genome3d.eu/
This contains C. elegans proteins and has 3D coordinates for all proteins produced by some of the best methods, including Phyre (mentioned in two posts above), all in one place. You can download PDB coordinates or view in your browser. It includes superpositions of all models and you can select which ones to include.
Do You mean getting a structure of a protein that hasn't been crystalized yet, but You got a sequence of it, and similar proteins in PDB?
In that case You can try homology modelling.
I think Phyre http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index is awesome. If not, try https://www.genesilico.pl/meta2/ or search for similar sites
Try I-Tasser http://zhanglab.ccmb.med.umich.edu/I-TASSER/ or SWISS-MODEL Workspace http://swissmodel.expasy.org/workspace/index.php?func=modelling_simple1. These servers need only fastа-format for input and do their own search for suitable three-dimensional models for pattern
Hi, there are many interesting tools doing this. Among them, I've tried Phyre, as mentioned by Jan. It gives you a pdb file, which you can visualize for instance with raswin or Swiss-PdbViewer. By the way, I guess that you can do the same through swissprot; sorry but I didn’t bookmark the page.
Alernatively, you may use programs like Raptor X (http://raptorx.uchicago.edu/) which proposes you different models according to the template used from Pdb. It’s very easy to use and I found it quite convincing. You may also try the GeneSilico Metaserver (https://genesilico.pl/toolkit/index).
Good predictions, Sébastien.
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