hello, proper domain orientation can be imposed during modeling if you use the the full structure , two domains, simultaneously. In this way interdomain restraints will be derived from the template and applied to your target. Andras Stefano Ciurli wrote: > > I have the following question: > I wish to model a series of homologous proteins (28 in total) for > which I have the structure of the first and the 26th in order of > sequence homology (ranging from ca. 55% to ca. 20%). The protein is > made of two domains. The two available structures are quite similar > except for the orientation of one domain with respect to the other > (significantly off). What is the best approach to model sequences #2 > to #25 and #27-#28??? Is there an accepted protocol in order to model > multidomain proteins? I know that one of the biggest problems with > modelling protein structures is encountered when you have more than > one domain, that is, to model relative domain orientation. Is there a > way out? How would you proceed using Modeller??? -- , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras