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Open Access Research article

Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands

Keisuke Ueno1, Katsuhiko Mineta2, Kimihito Ito1 and Toshinori Endo2*

Author Affiliations

1 Division of Bioinformatics, Hokkaido University Research Center for Zoonosis Control, North 20 West 10, Sapporo, Hokkaido, 001-0020, Japan

2 Graduate School of Information Science and Technology, Hokkaido University, North 14 West 9, Sapporo, Hokkaido, 060-0814, Japan

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BMC Structural Biology 2012, 12:5  doi:10.1186/1472-6807-12-5

Published: 26 April 2012

Additional files

Additional file 1:

Table S1. Descriptions of the oxidoreductases mapped onto the SOM. File “TableS1.xls” contains results of the SOM of oxidoreductases. The 4,092 RDFs were mapped onto a [46, 28]-sized rectangular lattice. The columns include a map position of a PDB code with functional annotation.

Format: XLS Size: 1.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Table S2. Descriptions of the transferases mapped onto the SOM. File “TableS2.xls” contains results of the SOM of transferases. The 1,444 RDFs were mapped onto a [40, 19]-sized rectangular lattice. The columns include a map position of a PDB code with functional annotation.

Format: XLS Size: 223KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Figure S1. The SOM labeled with the EC numbers of oxidoreductases. File “FigS1.pdf” contains results of the SOM of oxidoreductases. The 4,092 RDFs were mapped onto a [46, 28]-sized rectangular lattice, where each color of the node shows the major EC number in a node. The details of catalytic sites mapped onto the SOM were described in Table S1.

Format: PDF Size: 314KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Figure S2. The SOM labeled with the EC numbers of transferases. File “FigS2.pdf” contains results of the SOM of transferases. The 1,444 RDFs were mapped onto a [40, 19]-sized rectangular lattice, where each color of the node shows the major EC number in a node. The details of catalytic sites mapped onto the SOM were described in Table S2.

Format: PDF Size: 73KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Table S3. Confusion matrix of the SOM for the EC numbers of oxidoreductases. File “TableS3.xls” contains the confusion matrix of the SOM for the EC numbers of oxidoreductases. Each column of the matrix shows the number of RDFs in the assigned EC number, and rows represent the oxidoreductase list of the actual EC numbers.

Format: XLS Size: 391KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Table S4. Confusion matrix of the SOM for the EC numbers of transferases. File “TableS4.xls” contains the confusion matrix of the SOM for the EC numbers of transferases. Each column of the matrix shows the number of RDFs in the assigned EC number, and rows represent the transferase list of the actual EC numbers.

Format: XLS Size: 106KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Figure S3. An example of an RDF. File “FigS3.pdf” contains an example of an RDF for the total charge, σ-electronegativity, π-electronegativity and effective atom polarizability, which constitute a 160-dimensional variable as a feature vector.

Format: PDF Size: 37KB Download file

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Additional file 8:

Figure S4. Robustness of functional classification to conformational change. File “FigS4.pdf” contains the performance of the SOM clustering for the EC numbers as a B-factor in the RDFs is varied. The large B-factor in the RDFs corresponds to conformational change. The F-measure indicates the robustness of the classification performance.

Format: PDF Size: 16KB Download file

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Open Data