All of the protein structure prediction servers (that I am familiar with) do not appear to work for metalloproteins in general, e.g. I-Tasser. Since metalloproteins are half of all proteins this is a major limitation. The protein I am trying to model has a known Zn finger.
Sir please check this link there are few software that might help you. As donald lab is concerned with 3d structure predictions of metalloproteins...
http://www.cs.duke.edu/donaldlab/people_shu.php
Try Swissmodel and or modeller
http://swissmodel.expasy.org/interactive
https://salilab.org/modeller/tutorial/
Thank you, Anum Munir, for your suggestion. The Duke link was indeed interesting but there is no link to any software that could be useful. Even the link in the published paper (www.fos.su.se/~nanjiang/zincpred/download/ ) is not functional. I already know the aa involved in the Zn-binding (as well as the geometry). I would like an optimal 3D model of the protein with these constraints built in.
Sir you can use Rosetta 3 software. Link of one of the related paper to this is
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866275/
- Badges
- Science method