In the tests above only the type and length of secondary structures, the loop length observed in the query structure, and the pattern of burial and exposure, observed or predicted for each secondary structure segment were used in the search. Many published predictions are augmented by human insight, contain detailed predictions of loop lengths, and consider experimental distance restraints. All of this information can be used with the MAP method described here. To test the method under these circumstances, we considered three predictions: 1) the von Willebrand factor (vWf) prediction by Edwards &Perkins (1995), 2) the Proteasome prediction by Lupas et al. (1994) and 3) a prediction for the Phosphotyrosine Interaction Domain (PID) by Bork &Margolis (1995). All of these predictions were made from very diverse sequences, which is likely to improve prediction accuracy [Russell \& Sternberg, 1995]. The predictions also comprise carefully constructed sequence alignments, that can provide tight loop-length distance restraints. For the three searches, a larger and more up-to-date database of 780 protein domains was scanned (A. S. Siddiqui per. comm.) Subsequent 3D structure determination has shown all three of these proteins to resemble previously observed folds [Zhou et al., 1995][Brannigan et al., 1995][Lee et al., 1995].