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

Download Software

Please kindly send suggestions, post questions, and report bugs to Zeyar Aung (azeyat A_T i2r.a-star.edu.sg, zeyarag A_T gmail.com).

· Win32 (Complied and tested under Windows XP)
- Unzip it with WinZip or 7-Zip (a freeware available at: www.7-zip.org/ )
- 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)

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Last Update: Wednesday, August 02, 2006