Method
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database
- † Equal contributors
1 Institute of Bioinformatics, National Chiao Tung University, 75 Po-Ai Street, Hsinchu, 30050, Taiwan
2 Department of Biological Science and Technology, National Chiao Tung University, 75 Po-Ai Street, Hsinchu, 30050, Taiwan
3 Core Facility for Structural Bioinformatics, National Chiao Tung University, 75 Po-Ai Street, Hsinchu, Taiwan
Genome Biology 2007, 8:R31 doi:10.1186/gb-2007-8-3-r31
Published: 3 March 2007Additional files
Additional data file 1:
Table listing 674 protein pairs.
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Additional data file 2:
Figure showing the representative 3D fragments of the 23-state structural alphabet.
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Additional data file 3:
Figure showing the distributions of a 23-state structural alphabet on each kind of eight DSSP secondary structure codes.
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Additional data file 4:
Table showing the rmsd between X-ray structures and reconstructed structures using 23 representative segments on 38 proteins.
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Additional data file 5:
Figure showing an overview of 3D-BLAST for structure database search.
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Additional data file 6:
Table listing the average precision of each program on 108 queries in SCOP-108.
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Additional data file 7:
Table showing the recognition performance of nine methods on the Lindahl's benchmark dataset at the family, superfamily, and fold levels.
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Additional data file 8:
Table listing 976 proteins of the Lindahl's benchmark.
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