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 residue assignment and structure superposition for protein structure alignment, PLoS ONE, 7(5): e37493, 2012. (open access)


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