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Visualisering på internet av dockning av molekyler
Molecular docking program and molecular structure visualisation on the web
The understanding of protein structures have developed rapidly since the late 1950's. Today about 20.000 protein structures are known and there are realistic projections that all existing protein folds will be represented in the database within the near future (see Berman et al). The vast information available in the PDB database is a treasure-trove for humanity and work is underway to translate this treasure to useful applications. One important current development is to predict and analyze interactions between proteins and their substrates (from small organic molecules, such as medical drugs, to much larger substrates such as other proteins). Many different strategies for molecular docking has been developed and even more computer programs are available that implement those strategies (Halperin et al).
Specific plan and suitable previous knowledge:
The great number of available strategies and computer programs makes it hard to perform systematic analyses and evaluations of docking predictions. The aim of this project is to create a web interface that would collect available implementations of molecular docking together with molecular structure databases and facilitate systematic analyses. The project is suitable for two students or more. One student probably needs previous knowledge about php, linux server administration and mysql. The other student probably needs previous knowledge about computer graphics and molecular visualization, web design, and protein structures. Overlapping experiences, as well as experience with molecular docking is obviously an advantage.
Berman, Goodsell and Bourne, American Scientist 90 (4), 350 - 359 (2002)
Halperin et al, Proteins 47, 409-443 (2002)
Molecular docking, protein structure, web design, computer graphics, php, mysql, rational drug design.
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