Use of a structural alphabet for analysis of short loops connecting repetitive structures

doi:10.1186/1471-2105-5-58

BMC Bioinformatics

Volume 5

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Research article

Use of a structural alphabet for analysis of short loops connecting repetitive structures

Laurent Fourrier^* , Cristina Benros^* and Alexandre G de Brevern

Equipe de Bioinformatique Génomique et Moléculaire (EBGM), INSERM E0346, Université Denis DIDEROT-Paris 7, case 7113, 2, place Jussieu, 75251 Paris Cedex 05, France

author email corresponding author email* Contributed equally

BMC Bioinformatics 2004, 5:58doi:10.1186/1471-2105-5-58


Published:	12 May 2004

Additional files

Additional File 1:

Supplementary data 1: Comparison between the secondary structure assignments (file_1.rtf). file_1.rtf is a Rich Text Format file. It contains the example of the 6 assignment methods for the proto-oncogene Mtcp-1 (PDB code 1A1X chain A), see Figure 2 for details.

Format: RTF Size: 11KB Download file

Additional File 2:

Supplementary data 2: Representation of the secondary structure assignments (file_2.doc). Example of the proto-oncogene Mtcp-1 (PDB code 1A1X chain A), see Figure 3 for details.

Format: DOC Size: 105KB Download file

This file can be viewed with: Microsoft Word Viewer

Additional File 3:

Supplementary data 3: Description of Protein Blocks in the databank and in the loops (file_3.xls). file_3.xls is an Excel file. For each protein block (PB; labeled from a to p), we report the occurrence frequency (frq) in the overall database and in the loops set, the four main PB transitions and the distribution in the secondary structures (α-helix, coil and β-strand) of the central residue assigned by PSEA.

Format: XLS Size: 27KB Download file

This file can be viewed with: Microsoft Excel Viewer