Beta-Sheet's World
Figure 1. Ribbon diagram of
the beta-1 domain of streptococcal protein G (PDB code
1FD6). Alpha-helices are in red while beta-strands are in gold. The
image was produced using RasMol [1], Molscript [2] and Raster3D [3].
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Beta-Sheet's World is the homepage for various beta-sheet related proteomic tools.
Here are the available tools:
Beta-Sheet Annotation
- Beta-Spider annotates the beta-sheet domains of a PDB file.
Beta-Strand Shuffling
- Beta-Strand Shuffler generates all N! * 2^(N-2) possible strand topologies. For each topology it then generates all inter-strand registers. Each configuration is assigned a pseudo-energy value. The program can also generate input files for the Beta-Sheet Proposer/Builder. Baker's Top7 [4] protein beta-sheet is given as an example.
Beta-Sheet Construction
- Beta-Sheet Proposer generates 3D atomic coordinates from a beta-sheet 2D descriptor. The sheet topologies are limited to those found in the PDB.
- Beta-Sheet Builder generates 3D atomic coordinates from a beta-sheet 2D descriptor. The sheet topologies are not limited to those found in the PDB, and Baker's Top7 [4] protein beta-sheet is given as an example.
Beta-Sheet Helix Dressing
- Beta-Alpha-Beta dresses a beta-sheet with helices in a beta-alpha-beta motif. Baker's Top7 [4] protein beta-sheet and helices is given as an example.
Simple Tutorial on Protein 3D Modeling
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[1] R. A. Sayle, E. J. Milner-White, Rasmol: Biomolecular graphics for all, Trends Biol. Sci. 20 (1995) 374-376.
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[2] P. J. Kraulis, Molscript: a program to produce both detailed and schematic plots of protein structures, Journal of Applied Crystallography 24 (1991) 946-950.
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[3] E. A. Merritt, D. J. Bacon, Raster3D: Photorealistic Molecular Graphics, Methods in Enzymology 277 (1997) 505-524.
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[4] B. Kuhlman, G. Dantas, G. C. Ireton, G. Varani, B. L. Stoddard, D. Baker, Design of a novel globular protein fold with atomic-level accuracy, Science 302 (2003) 1364-1368.
Marc Parisien
14/07/2004 last update: 30/11/2004