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
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,
Department of Chemistry
Simon Fraser University
8888 University Drive