On Mon, Jul 05, 2004 at 03:00:34PM +0530, Himanshu Grover wrote: > i wish to know whether modeller can be used as a general optimization > tool. I have a structure of my protein... also know its binding site to > another protein (its a protein-protein complex). i just want to apply > simulated annealing to the binding site of my model, to find the best > binding conformation... can modeller do that for me??

Sure, you can do that - see question 12 in the FAQ: http://salilab.org/modeller/FAQ.html#12

> firstly, do i need to use the restraints generated by modeller... if yes, > which ones??

You can use whichever restraints you choose. You can add your own restraints, or override the default restraints with your own restraints file if you like - this is also in the FAQ.

> secondly, what new restraints, if at all, should be applied(as a part of > special restraints).

That depends on whether your template gives you enough information to generate all the restraints you need - it depends on your system.

> thirdly,is it necessary to use homology basis, the alignment, templates, > and homology derived restraints...??

It's not necessary to use homology-derived restraints; Modeller can use the CHARMM 22 force field and do standard MD if you like (although if you want to go down this road, you're probably better off using a dedicated MD package like CHARMM or GROMOS, and bear in mind that with MM force fields, such 'refinement' without template information is likely to lead to a worse structure). If you have a template, you probably want to use it.

Ben Webb, Modeller Caretaker