contact map generation?

ketchup Ketchup at cris.com
Tue Jan 21 18:08:33 EST 1997



PSdbView presents the information graphically, I don't know if
there is a way to get the table printed and David Deerfield.

Requires JAVA capable viewer.

http://www.psc.edu/~geigel/PSdb/PSdb.html


That info will also be in Steven Bryant's thresding database - under
research projects on the NCBI web site.



iropson at bcmic.hmc.psu.edu (Ira Ropson) wrote:

>Hello,

>Is there an easy way to construct a contact map for a protein of known
>structure in the PDB? I'd like to know and compare the nearest neighbor
>amino acids to a particular residue in a family of proteins with very
>similar structures but only 25% or so sequence identity. I could
>construct a table of interacting residues manually, by specifying a
>sphere of say 5 angstrom radius around the residue that I am probing in
>insightII or rasmol and then identifying those amino acids that are in
>that sphere. However, I can't help but think that there must be a
>better way to evaluate the entire structure at once, and that someone
>has written a program to do this for me.

>Thanks in advance.
>Ira Ropson
>iropson at bcmic.hmc.psu.edu
>If I had time for a fancy Sig file I problably wouldn't have a job.






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