I would like to know which will be the best server or tool, to predict protein structure by ab initio modeling. Kindly anyone help with this
You can explore Rosetta (https://www.rosettacommons.org/) or Phyre (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index).
But how far the structure will be reliable?
Reliability decreases as the sequence homology decreases. But u can rely on Rosetta than Phyre because Phyre is threading based structural modeling while Rosetta is completely ab-initio based.