Dear Zheng, There are some things you can try, which depend on the computational resources you have available and the time you want to wait. The best would be to try Rosetta ab initio modelling. Preferably, you would run Rosetta using your local installation but if you don’t have Rosetta installed, this can be annoying to do. You can also use the Rosie web server (the Rosetta web server), but it takes long time to compute. Other faster solutions for "ab initio" modelling would be Quark (in case your protein is short), I-tasser or RaptorX Contact Prediction web servers. I am very happy with the latter, I use it frequently when I don’t want to wait for Rosetta. You can also try homology modelling, but this would be less reliable when the few motifs you find do not overlap and do not cover the entire protein. Anyway, for homology modelling you can try , for example, Modeller after HHPred (you can do this using the MPI Bioinformatics toolkit) or RaptorX Structure Prediction.
I hope this helps you. Best regards and good luck! Dr. Joana Pereira -- Postdoctoral Researcher Department of Protein Evolution Max Planck Institute for Developmental Biology Spemannstraße 35 72076 Tübingen GERMANY > On 06 Dec 2017, at 15:14, zheng zhou <[email protected]> wrote: > > Dear CCP4 community, > > Sorry for the off-topic question. I am trying to design constructs for > structure studies. It only has a homolog structure in PDB with > sequence identity ~20%. When I blast against PDB sequence, there are > quite a few motif hits (30~40aa, identity 40~50%). Any prediction > tools utilize this information? > > Thanks for your advice in advance. > > Best, > > Zheng
