SAS-Pro Homepage

The SAS-Pro software provides an optimal structural alignment between any given pair of proteins. It is based on an algorithm for Simultaneous Alignment and structure Superposition of PROteins (SAS-Pro). SAS-Pro provides both sequential and non-sequential protein alignments.


The algorithm of SAS-Pro is described in detail in the following paper:
S. B. Shah and N. V. Sahinidis, SAS-Pro: Simultaneous Alignment and Superposition of PROtein structures, submitted, 2011.


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:

  1. 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.
  2. 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

The SAS-Pro source code is freely available:

It has been tested on an INTEL Quad Core 2.83 GHz processor and provides average run times of 1 CPU minute per alignment. The software requires

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

Please contact Professor Nick Sahinidis if you have any comments or suggestions.

To Nick Sahinidis' Bioinformatics Software Web Site

To Nick Sahinidis' Optimization Group Web Site