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] |