This directory contains routines and scripts to run the design program
given a pdb file and a multiple alignment file.  The first sequence of 
the multiple alignment should match the pdb file and contain no gaps.
The progam blastpgp is required to generate a position specific scoring 
matrix (PSSM) from the alignment.

To compile the c++ programs, go to the "src/" directory and 
type the clean and make command.

         % ./clean
	 % make

Program paths in several perl scripts in "src/" directory should be changed
to the "src/" directory of this design package on your machine. 

These paths are:
$path in src/design.perl (default is "/home/jpei/sd/src/")
$path in src/all_h.perl (default is "/home/jpei/sd/src/")
$path in src/all_v.perl (default is "/home/jpei/sd/src/")
$path in src/opw.perl (default is "/home/jpei/sd/src/")

For example, if you have installed this design package in your directory 
of "/home/tom/design/sd/", the above paths should all be changed to 
"/home/tom/design/sd/src/".

The blastpgp program in src/design.perl should also be changed to the blastpgp 
on your machine. (default is "/data/usr1/seals/bin/blastpgp")

The script for automatic design is design.perl, which takes the first and
the second arguments as pdb file and alignment file, respectively.  Other
options can define other design parameters.

    -d: the evolutionary distance from the designed sequence to the
	original sequence (average number of substitutions per position), default: 1
    -run: the number of sequences to be designed, default: 70
    -step: number of accepted mutations, default: length of the protein
    -T: temperature, default 0.13
    -seed: seed for starting the random number, should be a negative 
	   integer.
    -w: weight between Miyazawa-Jernigan term and PSSM term

It is important that the sequence in the pdb file should match exactly the first 
sequence in the alignment file.

There is an example in the directory 1an8/.

     ../src/design.perl 1an8.pdb 1an8.aln -d 2 -run 50

The designed sequences are in the file: ac_step***.aln, where *** is the
accepted mutation steps.  The design paramters are in the file design/info.

If you want to design sequences for a pdb file and an alignment, it is highly
recommended that you set up a directory to put these two files and run the 
design program in that directory. The design program will make several 
directories to store data and intermediate results in the current working 
directory.

For questions, please contact: jpei@chop.swmed.edu

Information about this program can be found in the following article:

Pei J, Dokholyan NV, Shakhnovich EI, Grishin NV: Using protein design 
for homology detection and active site searches.  Proc Natl Acad Sci 
U S A 2003, 100:11361-11366.

