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Team:Goettingen/project overview/project drylab
From 2014.igem.org
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| - | <a href="https://static.igem.org/mediawiki/2014/8/8e/Goettingen-Drylab-graphic.jpg" target="1"><img src="https://static.igem.org/mediawiki/2014/8/8e/Goettingen-Drylab-graphic.jpg" width="700" /></a><center><br /><p align = "justify">Figure:Depicting the procedure for Homology modeling: All peptides were cloned inside a scaffold (B1 domain of protein G from <i>Streptococcus aureus</i>. The peptides were short enough to be modeled as an internal loop by loop refinement; however, these structures should only be considered as a working model, since we don't have direct crystallographic data.</p></center><br /><br /> | + | <a href="https://static.igem.org/mediawiki/2014/8/8e/Goettingen-Drylab-graphic.jpg" target="1"><img src="https://static.igem.org/mediawiki/2014/8/8e/Goettingen-Drylab-graphic.jpg" width="700" /></a><center><br /><p align = "justify"><b>Figure:</b>Depicting the procedure for Homology modeling: All peptides were cloned inside a scaffold (B1 domain of protein G from <i>Streptococcus aureus</i>. The peptides were short enough to be modeled as an internal loop by loop refinement; however, these structures should only be considered as a working model, since we don't have direct crystallographic data.</p></center><br /><br /> |
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Revision as of 17:16, 19 September 2014
Project
9/15 
Dry lab
Homology modelling
We modeled the 3D structure of our peptide-containing scaffolds (domain B1 of protein G from Staphylococcus aureus) by homology modelling. We used Modeller library to accomplish that; since the peptide is about 20-25 amino acid residues long, it can be modeled as a loop inside the B1 domain scaffold for which there are already a number of 3D structures available at the Protein Data Bank.
Figure:Depicting the procedure for Homology modeling: All peptides were cloned inside a scaffold (B1 domain of protein G from Streptococcus aureus. The peptides were short enough to be modeled as an internal loop by loop refinement; however, these structures should only be considered as a working model, since we don't have direct crystallographic data.
References
- 1. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.
- 2. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.
- 3. A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.
- 4. A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000.
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