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# SAS-Pro: Simultaneous Alignment and Superposition of PROtein structures
# Authors: Shweta B. Shah and Nick Sahinidis
#
# Date: June 2011
#
# Contact nikos@gatech.edu with any questions about the software
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The SAS-Pro software provides optimal structural alignments between any
given pair of proteins. SAS-Pro provides both sequential and non-sequential 
alignments between the two proteins. 

The inputs are the PDB files  and, optionally, the chains of the two
proteins to be compared.  The output includes best alignment, the RMSD 
value, the SAS value, the length of alignment, and the aligned protein 
structure cordinates.

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Software requirements:
1. Licensed copy of MATLAB 6 or newer version on Linux/Unix
2. gfortran compiler 4.4.1 or newer version

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Installation Instructions for SAS-Pro:
======================================
1. Download SAS-Pro.tar 
2. Untar using 
> tar -xvf SAS-Pro.tar 
3. Run the installation file 
> ./make install
4. To uninstall run make clean
> ./make clean
5. To run a test problem run make test
> ./make test

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Running SAS-Pro:
================
SAS-Pro runs with the command:
SAS-Pro_PATH/bin/saspro [protein 1] [protein 2] [chain of protein 1] [chain of protein 2]

INPUTS:
=======
[protein 1]            := The PDB file for protein 1  
[protein 2]            := The PDB file for protein 2
[chain of protein 1/2] := The chain of the input protein that should be aligned

OPTIONS:
========
[chain of protein 1/2]: This is optional. If none is mentioned, the first chain 
                        in the PDB file will be chosen.

OUTPUTS:
========
The final alignment is written in file ALIGN in the current directory. The 
corresponding sequential alignment is written in file ALIGN_SEQ in the current 
directory. The C-alpha cordinates o aligned proteins are written in file 
PROTEIN-CORDS. The values of RMSD, SAS, and Length of Alignment are available 
at the bottom of files ALIGN and ALIGN_SEQ.

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Test problems:
==============
All PDB files for proteins in the Sokol, Skolnick, and RIPC data sets are 
available in the folder `test'. A test problem can be run to check all 
options by running ./make test.

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Usage and license requirements
==============================

Use of this software requires that the following papers be cited in any
resulting publications:

1. S. B. Shah and N. V. Sahinidis, SAS-Pro: Simultaneous residue alignment and 
   structure superposition for protein structure alignment,
   PLoS ONE, 7:e37493, 2012. 
2. W. Huyer and A. Neumaier, SNOBFIT: Stable noisy optimization by branch 
   and fit, ACM Transactions on Mathematical Software, 2008, 35, 1-25.
3. M. Dell'Amico, A. Lodi, S. Martello, Efficient algorithms and codes
   for the k-cardinality assignment problem. Discrete Applied Mathematics,
   2001, 110, 25-40. 

Licenses

The SAS-Pro routines are provided free with no restriction on their use.
However, the current SAS-Pro distribution includes (with permission)
two software that impose usage/license requirements:

a. The SNOBFIT derivative-free solver that was developed by Huyer and
Neumaier (2008) is included in SAS-Pro for solving a multimodal, 
non-smooth optimization problem. This solver may be used freely with
proper acknowledgment but is Matlab-based and requires a licensed 
copy of Matlab.

b. The SKAP code is used in SAS-Pro to solve k-cardinality linear 
assignment subproblems. SKAP and the subroutines that it calls are 
copyright Dell'Amico-Lodi-Martello (2001). Permission to use SKAP
and the associated code for didactic and scientific purposes is granted 
provided proper acknowledgment is given. For commercial use of SKAP,
contact silvano.martello@unibo.it.