Modeller users:

As a neophyte, both to homology modeling and to the program Modeller-4, I am somewhat confused by the protocol to follow in order to generate a model of my target enzyme. I would be very grateful if the Modeller user community could help get me going!

I have the sequence of my target, and five .pdb files of enzymes that belong to the same family, and share between 30 - 50% sequence similarity to the target. I want to get a 'good' model of the target - CPU time is not a problem, I would prefer to be thorough and get better results.

Can anybody suggest the procedure I should follow, from the beginning!

What file do I begin with? Do I write this myself? What is it called? How do I obtain an alignment file? MALIGN-3D? then CHECK_ALIGNMENT? Which script files should I run? mod model-default? How do I account for the error noted in the newsgroup archives?

Any suggestions appreciated!

Similarly, if anyone has modified the basic script files to good effect, I would appreciate a copy!

Thanks in advance,

Nick

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Nick Glover Department of Chemistry Simon Fraser University 8888 University Drive Burnaby, BC V5A 1S6 Canada