I found that the "psipred" installed at three different places generated different results for one sequence (Rad59, please focus on the 40 aa at its N-terminus). Is that because their version? Which "psipred" is more reliable?
1. "Fragment Libraries" server (v2.6): http://robetta.bakerlab.org/downloads/fragments/22521/
2. the SYMPRED server (v ?): http://zeus.few.vu.nl/jobs/aeb9f401c184595c85e6ef7aaef6defe/
3. A local installed Psipred copy (v. 3.2 ?).
The secondary structure prediction will affect the fragment libraries. How much do the fragment libraries affect the final AbinitioRelax prediction?