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Table 1 Similarity scoring schemes distributed with homolmapper.

From: Flexible mapping of homology onto structure with Homolmapper

Scheme Location Description Reference
BLOSUM62 built-in BLOSUM substitution matrix [30]
PAM250 " PAM substitution matrix [31]
charge " sidechain charge at pH 7 --
nonpolar ASA external file nonpolar sidechain surface area [56]
hydrophobicity " ΔΔGtransfer relative to Gly [57, 58]
sidechain ΔS " sidechain entropy of folding [59]
simple charge " ± 1 charges (Asp, Glu, Lys, Arg) --
identity matrix " for use in development --
BLOSUM30 archive BLOSUM substitution matrix [30]
BLOSUM35 " " [30]
BLOSUM40 " " [30]
BLOSUM45 " " [30]
BLOSUM50 " " [30]
BLOSUM55 " " [30]
BLOSUM60 " " [30]
BLOSUM65 " " [30]
BLOSUM70 " " [30]
BLOSUM75 " " [30]
BLOSUM80 " " [30]
BLOSUM85 " " [30]
BLOSUM90 " " [30]
PAM20 " PAM substitution matrix [31]
PAM60 " " [31]
PAM120 " " [31]
PAM160 " " [31]
PAM350 " " [31]
Gonnet40 " " [32]
Gonnet80 " Gonnet substitution matrix [32]
Gonnet120 " " [32]
Gonnet160 " " [32]
Gonnet250 " " [32]
Gonnet300 " " [32]
Gonnet350 " " [32]
total ASA " total sidechain surface area [56]
partial volume " residue partial volume in solution [60]
volume " amino acid Van der Waals volume [60]
amino acid freq. " amino acid frequency [61]
exp. BLOSUM62* " adds standard 'B,' 'X,', 'Z' [30]
exp. PAM250* " " [31]
  1. Three substitution matrices are built-in to the homolmapper application ("built-in"), while the others are supplied as external matrices that can be loaded at runtime if so desired. Some of the external matrices are supplied in a compressed archive ("compressed"), while others are not ("external file"). The expanded BLOSUM62 and PAM250 schemes (*) incorporate standard values for 'B,' 'X,' and 'Z' amino acids.