Re: [ccp4bb] Modeling protein tertiary structure

Phyre2 absolutely deserves a mention. My 'threader' of choice. --- Antony W Oliver --- --- sent from my mobile account --- On 10 December 2016 at 00:05, Myeongseon Lee (이명선) <0e01bd27cd0f-dmarc-requ...@jiscmail.ac.uk> wrote: Hi, all. C

Re: [ccp4bb] Modeling protein tertiary structure

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

Re: [ccp4bb] Modeling protein tertiary structure

I would recommend Haddock Prof. em. Ylva Lindqvist Dept. of Medical Biochemistry & Biophysics Div. of Molecular Structural Biology KAROLINSKA INSTITUTET Tomtebodavägen 6 S-171 77 Stockholm, Sweden Phone +46 8 52487695 Mobile +46 708 264356 Fax +46 8 327626 Email: ylva.lindqv...@ki.se URL: htt

Re: [ccp4bb] Modeling protein tertiary structure

The easiest is modeller via chimera. You can use I-TASSER server but it decides for itself what to do... You have some control too. You can use the sec structure from itasser and then go to modeller in chimera You can use modeller in the interfaces it provides in the web (mod web ...) or modell

[ccp4bb] Modeling protein tertiary structure

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 struct