Subject: mapping sequence data onto know 2ndary structures

From: Paul Beroza <[email-masked]>
Date: Wed, 21 May 1997 09:37:10 -0700 (PDT)

A couple of weeks ago Dan Severance wrote:

>   I want to be able to quickly generate a given secondary structure
> from a sequence, and I'd like to do it nongraphically so I can generate
> a large number with little or no "human" intervention :-)
>    I'm not talking reality, per se, just a sequence and an identifier
> of some sort specifying that I want a generic beta sheet, gamma turn,
> etc.
>    I know how to do it graphically in various software packages, but
> I want to be able to generate these from an automated script.

I wrote a program, "peptide",  to do this.  It is in the NAB language 
(which was designed for nucleic acids, but can also be used for proteins) 

The command line syntax is:

% peptide  structure sequence < -lib libfile>

where "structure" defines the type of structure to be created and 
"sequence" is a string o of 1 letter amino acid codes.  For example:

% peptide ALPHA  AAAAA -lib conf.lib

will write out (in pdb format) the coordinates of an alanine pentapeptide 
in an alpha helical structure.

You must have the "nab" compiler:

  info on nab = http://www.scripps.edu/case.
  nab source  = ftp://ftp.scripps.edu/pub/macke/nab-2.1.tar.Z

Once you have the nab compiler installed, get the peptide package from

	ftp://ftp.scripps.edu/pub/beroza/peptide

I hope this is useful, and any comments and suggestions about the
program are welcome.

Paul
  
---------------------------------------------------------------------  
 Paul Beroza 
 The Scripps Research Institute        email: [email-masked]  
 Department of Molecular Biology       phone: 619-784-9957   
 10550 N. Torrey Pines Rd. - TPC15     fax: 619-784-8896   
 La Jolla, CA 92037                    URL: www.scripps.edu/~beroza  
---------------------------------------------------------------------