Software and Supplementary Information for the paper

MatAlign: Precise Protein Structure Comparison by Matrix Alignment

Journal of Bioinformatics and Computational Biology, 4(6):1197-1216, 2006

Zeyar Aung and Kian-Lee Tan

National University of Singapore


Download Software

Please kindly send suggestions, post questions, and report bugs to Zeyar Aung (zeyarag A_T


·        Win32 (Complied and tested under Windows XP)
- Unzip it with WinZip or 7-Zip (a freeware available at: )
- Consult MatAlign_v11_Readme.pdf as a user manual.


·        Unix (compiled and tested under SunOS 5.7)  
- After downloading the file, if its extension is ".tar" or ".tar.tar", please change it to ".tar.gz" before decompressing the file.
- Decompress it with gzip and tar
     gzip –d MatAlign_v11_Unix.tar.gz
     tar xvf MatAlign_v11_Unix.tar
- Consult README file and MatAlign_v11_Readme_Unix.pdf file.


Supplementary Information for the Manuscript

·        Although MatAlign also employs two-level dynamic programming as in SSAP (Taylor and Orengo, JMB 208, 1989), it is substantially different from SSAP.  (See details in Pdf)


·        MatAlign performs better than DALI and CE in terms of 4 alignment quality criteria in a majority of cases.  (See detailed results in MS Excel)


·        When the alignment lengths are set to be equal, MatAlign’s RMSD is still better in a majority of cases.  (See detailed results in MS Excel)


·        Classification Experiment at Super Family Level (20 query proteins against 200 database proteins).  (Download dataset in MS Excel)  (See detailed results in MS Excel)



Last Update: Wednesday, August 02, 2006