Zhang Server for Molecular Replacement
I have mentioned the Zhang server before and so thought I would share 2 ways this server can be helpful to crystallographers.
The Zhang Server (I-TASSER server) uses the amino acid sequence of a protein to predict its structure. The server is simple to use– enter in your desired amino acid sequence and email.
Note: You need to have an academic email address to use the server freely. (more information about the server).
Good:
1) Great resource: the server allows users to submit their sequences to be analyzed
2) Free to all academic users
Bad:
1) Turn around time: it took about two weeks before my predictions were complete (this will vary greatly depending on how many proteins are in the queue upon submission)
The two ways this server could be helpful:
First
I was able to find another protein that may have a similar fold to the one I am working on. Were it not for this server, this protein would have gone unnoticed. The Zhang server searches through the PDB looking for homology that you may miss.
Second:
In silico molecular replacement? Could the coordinates from the Zhang server then be used for molecular replacement? This idea is being explored by MR-CAFASP. I have not heard of many crystallographers testing whether in silico molecular replacement would work.
Has a novel protein been published using in silico predictions? In the future, I will play around with the coordinate file from the Zhang server to determine whether or not the results are robust enough to yield reasonable crystallographic statistics.