Reply To: Native gives higher (positive) than lowest energy and clustered decoys

[Anonymous]

It’s known that structures from the PDB, when scored directly with the Rosetta energy function, can give ludicrously high energies. The reason is that Rosetta is sensitive to small positional differences. (e.g. if two atoms are slightly closer than they should be – we’re talking fractions of an Angstrom – the VDW repulsive energy can shoot way up.)

It’s highly recommended to either minimize the structure (or use the regular relax application) in the Rosetta energy function prior to comparing energies between native and predicted structures.