Cadence Tutorial

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(New page: = Cadence Labs Synthetic Biology Tutorial = This page is to host discuss of the [http://www.cadence.com/company/cadence_labs/index.aspx Cadence Research Laboratory's] tutorial run by [htt...)
Current revision (01:17, 24 January 2008) (view source)
 
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= Cadence Labs Synthetic Biology Tutorial =
= Cadence Labs Synthetic Biology Tutorial =
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This page is to host discuss of the [http://www.cadence.com/company/cadence_labs/index.aspx Cadence Research Laboratory's] tutorial run by [http://synberc.org SynBERC] scientists, Chris Anderson, [[Arkin Lab | Adam Arkin]], John Dueber and Tanja Kortemme.
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This page is to host discuss of the [http://www.cadence.com/company/cadence_labs/index.aspx Cadence Research Laboratory's] tutorial run by [http://synberc.org SynBERC] scientists, Chris Anderson, [[Arkin Lab | Adam Arkin]], John Dueber and [http://kortemmelab.ucsf.edu Tanja Kortemme].
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* Introduction: Adam Arkin
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* [http://openwetware.org/wiki/Image:2008-01-14-Cadence2_Intro.ppt Introduction: Adam Arkin]
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* Classical DNA Manipulation: Chris Anderson
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* [[Media:011308-Historical Cloning | Classical DNA Manipulation:]] Chris Anderson
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* Parts: Computational Design of Protein Function: Tanja Kortemme
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* [http://openwetware.org/wiki/Image:08_TanjaKortemme_CadenceBiotutorial.pdf Parts: Computational Design of Protein Function: Tanja Kortemme]
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* Devices: Generic Design of Protein Interaction via Protein Scaffolds
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*[http://openwetware.org/wiki/Image:2008-01-14-Cadence2_Scaffolds.ppt Devices: Generic Design of Protein Interaction via Protein Scaffolds: John Dueber]
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* Systems: Therapeutic Bacteria: Chris Anderson
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* [[Media:011308-TKB section | Systems: Therapeutic Bacteria:]] Chris Anderson
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* Characterization and Systems: Adam Arkin
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* [http://openwetware.org/wiki/Image:2008-01-14-Cadence2.ppt Characterization and Systems: Adam Arkin]
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* Scale up of Manufacture: Chris Anderson
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* [[Media:011308-Modern Cloning | Scale up of Manufacture:]] Chris Anderson
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References:
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* Molecular Design
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** [http://openwetware.org/wiki/Image:HumphrisKortemme_PLoS_CompBio.pdf Optimization of Proteins for Multiple Fitness Criteria:] Humphris & Kortemme; "Design of Multi-Specificity in Protein Interfaces", PLoS Computational Biology 3(8): 1591-1604.
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** [http://openwetware.org/wiki/Image:KortemmeBaker_CurrOpinChemBiol.pdf Review Article on Molecular Design of Protein Interfaces:] Kortemme & Baker; "Computational design of protein–protein interactions", Current Opinion in Chemical Biology, Volume 8, Issue 1, February 2004, Pages 91-97. 
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** Optimization Methods: Voigt et al., "Trading accuracy for speed: a quantitative comparison of search algorithms in protein sequence design", Journal of Molecular Biology, Volume 299, Issue 3, 9 June 2000, Pages 789-803; doi:10.1006/jmbi.2000.3758.
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* Modular Design Logic
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** [http://openwetware.org/wiki/Image:DueberLim_COSB.pdf Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry:] Dueber, Yeh, Bhattacharyya, Lim; "Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry", COSB 2004(14): 690-699.

Current revision

Cadence Labs Synthetic Biology Tutorial

This page is to host discuss of the Cadence Research Laboratory's tutorial run by SynBERC scientists, Chris Anderson, Adam Arkin, John Dueber and Tanja Kortemme.


The first tutorial took place January 14, 2007. The purpose was simply to outline the current definition, status and challenges.



References:

  • Molecular Design
    • Optimization of Proteins for Multiple Fitness Criteria: Humphris & Kortemme; "Design of Multi-Specificity in Protein Interfaces", PLoS Computational Biology 3(8): 1591-1604.
    • Review Article on Molecular Design of Protein Interfaces: Kortemme & Baker; "Computational design of protein–protein interactions", Current Opinion in Chemical Biology, Volume 8, Issue 1, February 2004, Pages 91-97.
    • Optimization Methods: Voigt et al., "Trading accuracy for speed: a quantitative comparison of search algorithms in protein sequence design", Journal of Molecular Biology, Volume 299, Issue 3, 9 June 2000, Pages 789-803; doi:10.1006/jmbi.2000.3758.
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