Researchers use 'natural' system to identify proteins most useful for developing an effective HIV vaccine JExpMed
, where a window size of 10 and 9 were used, respectively, to accommodate the larger size of the proteins. These represent an increased degree of sampling as compared to the defaults for the Monte Carlo option provided by the COREX/BEST server. All other unspecified parameters were default values. Thus, each protein ensemble was composed of ∼8 × 10,000=80,000 partially unfolded states.
The accessibility and stability scores for the entire set of random 15-mers can then be averaged and compared to the accessibility/stability score for the 15-mer epitope of interest. Thus, the random set was an internal control for each epitope, specific for the epitope’s complete protein.
In addition to mismatches at the single residue level, we assessed the prevalence of full epitopes by aligning full epitope sequences to collections of patient sequences from LANL as described. Epitopes were aligned using an adapted Boyer-Moore alignment algorithm. Epitope prevalence was assessed in the context of zero permitted mismatches or one permitted mismatch between the epitope sequence and the collection of patient sequences.
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