A Tool for Structure Alignment of Molecules

Authors: Pei-Ken Chang, Chien-Cheng Chen and Ming Ouhyoung
Department of Computer Science and Information Engineering, National Taiwan University

Proc. of IEEE Sixth International Symposium on Multimedia Software Engineering (IEEE-MSE2004) Special Session on Bioinformatics, pp. 354-361, Miami, USA, Dec. 2004. (ISBN 0-7695-2217-3)
Experimental Results - Comparison with Other Alignment Tools

Test Data
 PDB idchaindomain# of C-alpha atoms 
8DFR-4DFRa 8DFR  186 
4DFRa 159 
1MBD-1MBA 1MBD  153 
1MBA  146 
1TIE-4FGF 1TIE  166 
4FGF  124 
1CID-2RHE 1CID  177 
2RHE  114 
1REIa-7FABl2 1REIa 107 
7FABl2nd101starting from 104 and ending at 204
1FXIa-1UBQ 1FXIa 96 
1UBQ  76 

Ref:     R. Blankenbecler, M. Ohlsson, C. Peterson, and M. Ringner,
"Matching protein structures with fuzzy alignments",
Proc. Natl. Acad. Sci. USA., 100(21), Oct. 2003, pp. 11936-11940.

Alignment results for a set of protein pairs in terms of RMSD of matched atom pairs and number of aligned atoms (N)