Modeling Workshop

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    Modeling Exercises

  • Chimera Procedures - Text

  • Chimera Scripts

  • Download template files (modeling_exercises)

  • Demonstration Example
    • Query sequence: 1NBL_A (gi 29726600) - Hellethionin D from H. purpurascens
    • Template: pfam00321_1nbl.val
    • This file represents the thionin domain found in higher plants. It consists of 10 sequences of the pfam00321 alignment including 3 structures, and also the aligned sequence of 1NBL_A. Since the structure of the query is known, this case will serve as a test of the method. The query is 55% identical to the master structure over 45 residues.

  • Practical Exercise
    • Query sequence: NP_501549 (query) - RAP homolog from C. elegans
    • Template: rap1.val
    • This file represents the RAP1 domain (cd04175), a member of the RAS family of oncogenes. The file contains 10 sequences of the cd04175 alignment including 2 structures, along with the aligned query. The query is 90% identical to the master structure over 167 residues.

Revised March 4, 2008