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
