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Conserv, The residue conservation score server

Jon Wright1 and Carmay Lim1,2

1Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
2Department of Chemistry, National TsingHua University, HsinChu, Taiwan

This server can be used to obtain conservation values (similar to ConSurf) for residues in a single protein chain. The method it uses is based on the ConSurf method but is a completely new implimentation and is described on this page

. For your target protein provide either a single chain PDB file or the 4 letter PDB code and the chain ID or a fasta format sequence that you would like the conservation results for. (Note: Currently we are taking only single chain PDB structures).

An example of the results for the 1CRN pdb entry chain A can be found on this page.

A point to note is that the conservation value is for the position not the actual residue, so for instance if you have a chain where it is a particular residue most of the time (e.g. Asp281 in 99% of cases) and you provide a chain where the 281 is a Glu then the returned conservation score will be a 9 because a residue, the Asp, is highly conserved at that position even if in your own submitted chain it was something different.

The conservation is returned on a scale of 1-9, where 1 is very variable and 9 is highly conserved.

Submission area choose option A or Option B or Option C:

Option A) For a single protein chain structure that is to be uploaded from a file.
Select pdb file to upload:

Option B) For known PDB archive entry with a protein chain.
Provide a PDB ID (4 chars): and a chain (1 char) to upload:

Option C) For a fasta format.
Please paste it into the box here, single letter codes only:

Conserv was created by Jon D. Wright and Carmay Lim and is hosted in the Institute of BioMedical Sciences, Academia Sinica, Taipei, Taiwan.

Code that this server uses can be obtained from github as wrigjz/conservation_python.

Conserv is hosted at The Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.