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Table 1 Amino acid specific weighting factors. Average optimised parameter for all amino acids obtained from the 5 cross validation runs for three different classes of protein complexes.

From: Optimised amino acid specific weighting factors for unbound protein docking

Amino Acid Antibody/Antigen Enzyme/Inhibitor Others
ALA 2.32 0.68 0.74
ARG 0.00* 1.70 1.09
ASN 5.23 0.49 0.92
ASP 0.00* 0.00* 0.00*
CYS 0.14 1.11 0.18
GLN 0.00* 0.00* 1.06
GLU 0.15 0.00* 0.00*
GLY 2.49 1.47 7.24
HIS 8.74 3.17 0.00*
ILE 6.83 2.30 4.34
LEU 0.02 3.24 4.83
LYS 0.67 0.59 1.29
MET 1.46 9.63 3.90
PHE 4.46 3.14 7.89
PRO 1.98 0.00* 1.13
SER 0.00* 0.00* 0.00*
THR 0.25 2.67 3.08
TRP 4.99 5.19 2.56
TYR 11.64 4.94 8.83
VAL 3.10 2.78 3.02
I1 -3.45 8.34 0.15
  1. * None of these values is exactly 0.0. The optimised weighting factors for these amino acids are between 0.0001 and 0.0008