How to judge docking success for two proteins without knowledge of native structure
If you are trying to dock two proteins, using a global search, with no knowledge of correct answer (native structure) , how does one judge a docking success?. When reporting benchmark results, for example, the native (or mock-native) structure is used to rmsd against, and the definition of docking funnel is based on I_rmsd, so judgement of docking success is always based on some known (native) structure (or correct answer). Starting with just two proteins arbitrarily place apart.