Solvation preference profiles suggest places where the alignment should be improved. Native proteins and deliberately misfolded models have a very large gap in solvation preference. Credible models have solvation preferences closer to native proteins than to misfolded ones. The alignment is iteratively improved to optimize solvation preference. The sidechain optimization in rotamer space also tries to minimize clashes in the core.
Few clashes is also an indication of a credible model.
Contributions from Liisa Holm, Burkhard Rost, Peer Bork and Chris Sander. Abstract by Liisa Holm, edited by Chris Sander.