(none)

Steven Brenner seb1005 at mbfs.bio.cam.ac.uk
Tue Jul 6 14:08:05 EST 1993


keck at ucxray6.berkeley.edu (Jim Keck) writes:


>  I'm looking for a program that will read a PDB file as input
>and will create a new file simply listing the residue number
>and the secondary structural conformation that it is in. Anybody
>know of any such program???

dssp, available from ftp.embl-heidelberg.de, in the directory 
pub/databases/protein_extras/dssp

A reference to the methods it uses is:

 W. Kabsch, C. Sander, "Dictionary Of Protein Secondary Structure -
Patte rn-Recognition Of Hydrogen-Bonded And Geometrical Features."
_Biopolymers_ 22:1 2 2577-2637 (1983).

Should do the trick for you (it writes out secondary structure, as
well as solvent accessibility & some bond angles).  Its algorithm for
determining secondary is pretty simple, but it is useful for many
tasks.



-- 
Steven E. Brenner               |  Department of Biochemistry      
seb1005 at mbfs.bio.cam.ac.uk      |  University of Cambridge         
Lab   +44 223 333671            |  Tennis Court Road              
Fax   +44 223 333345            |  Cambridge CB2 1QW, UK          



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