On 12:08 Tue 05 May , Anastassis Perrakis wrote: > Modeller is indeed an excellent program (so are some others) but, > without being an expert, I was told some time ago and I am still under > the impression, that homology modeling with 20% identity (and many > insertions and deletions as you point out) is a dark art. Being able to > suggest the identical fold with some threading algorithm, is likely all > you will be able to do. A homology based model might be too much to ask.
Try HHpred. It will do a profile-profile alignment (well, technically HMM-HMM) and optionally create a multiple-template-based model using Modeller, all with very little knowledge or input required on the user end. Evaluating the likely correctness afterwards is a different story... -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University
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