Comparative modeling

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    • August 20, 2013 at 6:08 am #1698
      Anonymous

        Hi everyone, I am trying to model one protein using template which is ~65% homologue, i used comparative modeling protocol given along with the software, my question is how many “nstructures” we have to make , what is the standard number, i used 1000 but it seemed never ending in my lap top, so i stopped that, what is the minimum number of nstructures i can apply? and after getting structure what other applications i have to use in-order to make it final? i am very new for Rosetta, suggestions would be very helpful for me, thank you.

      • September 22, 2013 at 7:11 pm #9313
        Anonymous

          MRH,

          A million structures is a number to feel great about. 100,000 is probably good. 10,000 works in some circumstances. As you said, 1,000 took forever on your laptop – we don’t suggest ever using a laptop (or desktop) for this sort of work. ab initio is intended to be used on cluster supercomputers of at least a few hundred processing cores…there’s really no way to do it on the hardware you have. Take a look at the ROSIE and Robetta webservers to see if they’ll serve your purpose? There is also a commercial Rosetta@cloud service.

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