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Besides using position dependent evolutionary and structural features, we also use position independent features such as (a) physicochemical property, (b) specific propensity of being endpoints of an SS segment, and (c) correlated contact potential, for each amino acid.
Specifically, physicochemical property has 7 values for each amino acid (shown in Table 1 from [ 68]); specific propensity of being endpoints of an SS segment has 11 values for each amino acid (shown in Table 1 from [ 69]); correlated contact potential has 40 values for each amino acid (shown in Table 3 from [ 70]).
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Indeed, it would be interesting for future studies to compare overall gene expression patterns of male versus female C57BL/6 mice to identify factors responsible for the sex-specific propensity of females to develop PAH.
The difference between cases with different mutations can be explained by different propensities to form deposits, as well as a region-specific propensity of cell populations to accumulate abnormal PrP even within the same family.
For both analysis and control subsets, we calculated the relative position-specific propensities of each amino acid (Px) at twenty residue positions on the 20-mer peptides.
It could be reasoned that higher variability of relative position-specific propensities of amino acids in epitopes is indicative of distinct and perhaps complex patterns of position-specific conservation of residues.
On the P10P10' dataset, we computed Px (or relative position-specific residue propensity) of each amino acid at the different residue positions along the 20-mer sequence.
However, when decomposing the MOR in specific levels, the propensity of prescribing recommended statins presented a higher degree of clustering at the HCC level than at the HCA level (MORHCC = 2.18 vs. MORHCA = 1.31).
29 Participant-specific propensity scores were estimated from a logistic regression model to predict the probability of statin prescription.
SSP (secondary structure propensity) is a method developed by Forman-Kay and co-workers to determine the residue-specific secondary structure propensity of IDPs based on their measured chemical shifts (49).
It may be that MHC disease associations are driven less by allele-specific antigen presentation and more by the propensity of specific haplotypes to undergo strategic epigenetic modifications.
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