Advanced Homology Modeling:

Modeling a Sequence to a Target Stucture with only 35 % Identity

Prerequisites :

Topics to be covered include

• I. Identify weak blocks of conservation by aligning multiple sequences from the superfamily.

• II. Identify regions of missalignment between the target and the unknown structures by generating a quick-and-dirty model. Correct the alignment constraints and make an improved model.

• III. Check that important active site and structural interactions are present. Inspect the model for misfolded regions.

• IV. Run an Eisenberg comparison of the fit of the primary sequence of the model to its own 3-D structure. Compare this to a similar comparison of the template sequence and structure. Evaluate these comparisons.

  Steps I - III are done with LOOK. Step IV is done with INSIGHT.

For more information, contact the instructor

Jon Goldberg (Postdoc in Buz Baldwin's Lab)
B439 Beckman Center
S. U. M. C.
Stanford, CA 94305

(415) 723-6902, FAX (415) 725-6044
goldberg@cmgm.stanford.edu
http://cmgm.stanford.edu/~goldberg