Email updates

Keep up to date with the latest news and content from Genome Biology and BioMed Central.

Open Access Method

Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database

Chi-Hua Tung1, Jhang-Wei Huang1 and Jinn-Moon Yang123*

Author Affiliations

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

For all author emails, please log on.

Genome Biology 2007, 8:R31  doi:10.1186/gb-2007-8-3-r31

Published: 3 March 2007

Additional files

Additional data file 1:

Table listing 674 protein pairs.

Format: PDF Size: 52KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional data file 2:

Figure showing the representative 3D fragments of the 23-state structural alphabet.

Format: PDF Size: 53KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional data file 3:

Figure showing the distributions of a 23-state structural alphabet on each kind of eight DSSP secondary structure codes.

Format: PDF Size: 26KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional data file 4:

Table showing the rmsd between X-ray structures and reconstructed structures using 23 representative segments on 38 proteins.

Format: PDF Size: 11KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional data file 5:

Figure showing an overview of 3D-BLAST for structure database search.

Format: PDF Size: 146KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional data file 6:

Table listing the average precision of each program on 108 queries in SCOP-108.

Format: PDF Size: 36KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

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.

Format: PDF Size: 11KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional data file 8:

Table listing 976 proteins of the Lindahl's benchmark.

Format: PDF Size: 198KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data