Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior

BMC Bioinformatics

Table 1 Ten most similar matrices to PMBEC out of all complete matrices from the AA Index Database.

Matrix Identifier	Cor.\|PMBEC	Cor.\|BLOSUM62	Description
HENS920104	0.64	0.96	BLOSUM50 [1]
KANM000101	0.63	0.96	OPTIMA [23]
JOHM930101	0.63	0.87	Johnson & Overington [24]
HENS920102	0.62	1.00	BLOSUM62 [1]
KOSJ950115	0.62	0.81	Koshi & Goldstein [25]
HENS920103	0.61	0.97	BLOSUM80 [1]
OVEJ920105	0.61	0.69	Overington et al. [26]
BENS940103	0.61	0.93	Benner et al. [27]
VOGG950101	0.61	0.93	Vogt et al. [28]
GONG920101	0.61	0.93	Gonnet et al. [29]

From the AA Index Database [14], all complete 135 amino acid similarity matrices out of 141 were downloaded and compared to PMBEC based on their Pearson's correlation coefficients in the second column. See Methods for details. Also shown are correlation coefficients with respect to BLOSUM62 in the third column.