Figure 3

Comparison of sequence-based and structure-based alignments for T24/ubc9, T9/csc, and T28/egi. For each target, the percentage identity to the template is given based on an alignment after structure comparison, and the sequence alignment we used at CASP. Identities are indicated by "*". For all cases, the structure-based alignment, generated using the ALIGN [66] or CE programs [67], results in a lower similarity/percentage identity score between the target and template proteins. An all-atom conditional probability discriminatory function is able to readily distinguish a model constructed using the accurate structure-based alignment from one that is constructed using the sequence-based alignment.