Dear Myeongseon, my favourites are SwissModel (especially good for modelling close homologues, since it keeps conserved side chains & backbone as in the template; very fast (5-50 min), nice interactive user interface) RaptorX (good for more remote homologues too, also gives you secondary structure and disorder predictions, which I found very useful; takes a couple of hours to run). I-Tasser (probably the best for more remote homologues, but also slowest, and you can only submit 1 job at a time online; also predicts ligands, EC numbers & GO terms). @TOME (has some nice features for ligands to proteins). If time is not an issue, I'd just use all those (or more) servers in parallel. When superimposing the models, you can easily see where all servers predict the same model, and where they differ. The local rmsd gives you a good impression of how confident you can be in the model's different regions.
best wishes Stefan On 10 December 2016 at 00:05, Myeongseon Lee (이명선) < 00000e01bd27cd0f-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi, all. > > Could you anyone recommend me modeling programs for protein tertiary > structure? > > I have 3D strunture of a template protein and amino acid sequence of my > protein. These two proteins are very close structurally and functionally. > > I have done this kind of modeling with template 3D structure and amino > acid sequence of an unknown structure long time ago for other project. But, > unfortunately, I could not remember what program I have used at that time. > > Have a great day. > > > Sent from my Samsung device >
