I would recommend Modeller http://www.salilab.org/modeller/
Wai
Suppose I have two proteins A and B, they are structurally homologous, however the sequence identity is only about 20%. A has crystal structure available, so if I want to model protein B, what's the best way to do it? I don't think I can just thread the sequence of B to A structure because the number of residues are different and there might be gaps and insertions in the alignment. Any suggestions of good programs?
-- Yu Wai Chen, PhD........................................Lecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.
