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Dear all, thank you very much for all the responses to my inquiry. Among the mentionings, Modeller has the most recommendation - I was amazed by its capacity after getting around with the alignment settings! http://salilab.org/modeller/modeller.html Other recommentations are listed below - I haven't been able to test all of them but would like to share the information as my appreciation. Happy Holidays! -yong Robetta, here's the link: http://www.robetta.org/ Chainsaw within CCP4i SwissModel http://swissmodel.expasy.org//SWISS-MODEL.html. 3DPSSM? http://www.sbg.bio.ic.ac.uk/~3dpssm/ On 12/15/06, Yong Tang <[EMAIL PROTECTED]> wrote:
*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Dear all, I have a protein that has a homolog with known crystal structure. I aligned them manually and very carefully to make sure that we get what we have known right. I want to now replace the conserved residues in the model into those of my protein of interest and hopefully also do some sort of positional minimization so that I could have a rough idea about the surface of my protein of interest. Would there be any program doing this for me - that is, take the model pdb and my alignment file and generate a model for my protein of interest? If not, would you be kind enough to share your protocol with me if you have done this by hand. Happy Holidays! Thanks! -yong
