DASEY is used to align and score a probe sequence with a known template structure. This is achieved with PDFs of the form P(res

,ss

,

**DASEY**,res

_{j}*,*ss

) (Eq.

**5**), that give the likelihood of aligning residue type (res)

*j* of the probe to structure position

*i* of the template. This PDF depends on DASEY, res, and secondary structure type (ss). In the example of a DAPS aligned residue pair shown in Step 2, position

*i* of structure I, which happens to be occupied by a valine in a sheet (E) with a DASEY of [30, 56, 25, 48] and PHD () predicted secondary structure of sheet (E) is aligned to position

*j* of structure J, an arginine in a coil (C) with a DASEY of [32, 53, 20, 41] and PHD-predicted secondary structure of helix (H). The DASEY of [32, 53, 20, 41] means that the weighted sum of atomic solvation parameters for atoms within the Cα→N petal is 32, and so forth. Notice that the DASEY vectors from the aligned residue pair contribute to two bins. We place the DASEY vector [30, 56, 25, 48] from position

*i* into the first bin, which we denote “VE RH.” This means this DASEY represents a valine strand aligned to an arginine-predicted helix. Next we place the DASEY vector [32, 53, 20, 41] into a second bin, which we denote “RC VE.” Appropriately binned DASEY vectors from the training set of aligned known structures give density plots as shown on the left in Step 4. The distribution of DASEY values in each of the 3,600 bins (one bin for each combination of residue, predicted secondary structure, aligned residue, aligned secondary structure) is modeled as a mixture of multivariate normal PDFs, as shown by the equation on the right in Step 4. These density functions are the dominant terms of the emission score and describe the likelihood of aligning a residue and predicted secondary structure from a probe sequence of unknown structure with a residue, secondary structure, and DASEY from a template structure.

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