[modeller_usage] generating homology models of reduced disulfide bonds

[Stephanie Schaefer <saschaef AT UDel.Edu>]

Hello,

I recently obtained the xray structure of my wildtype protein which I am using as my template.  This protein has a redox active disulfide (an other structural disulfides).  I would like to generate homology models in which the redox active disulfide bond is broken (the model would represent the cysteines in a reduced environment).

I am new to modeler, but what I have done is edited the template PDB (wildtype) to remove the active site disulfide (SSbond) and then generated a homology model using the modified wt PDB as the template.  Is this the correct approach to generating a reduced active site model?

If this is not an acceptable approach what would you suggest?


Thank you for your time,
Stephanie Schaefer


University of Delaware
Biochemistry PhD Student
302-831-2658