Skip to main content
. Author manuscript; available in PMC: 2012 Jun 1.
Published in final edited form as: Chem Biol Drug Des. 2011 Apr 26;77(6):431–440. doi: 10.1111/j.1747-0285.2011.01111.x

Table 4.

Computational approximate binding affinity ranking for Peptides II–IX.a

Peptide
#		 Peptide Name Approximate
Binding
Affinity Rankb 		K*
VIII W1/W4/A9 1 3.89 × 10−8
VII W4/A9/W13 2 1.28 × 10−11
II Parent 3 4.27 × 10−12
IX W1/W4/A9/W13 4 2.39 × 10−13
I Linear 5 3.08 × 10−81
III W4/A9 1’ 2.42 × 10−1
VI SQ086 2’ 1.10 × 10−5
V SQ059 3’ 6.56 × 10−6
IV SQ027 4’ 1.50 × 10−7
a

The approximate binding affinity, K*, is a computational ranking parameter whose absolute value depends on statistical sampling and does not directly correspond to experimental binding affinities. For the new designs, Peptides VII, VIII, and IX, one of the positive controls, Peptide II, and the negative control Peptide I, 1000 peptide structures were predicted for each sequence, 1000 docked complexes were generated for each docking run, and the final peptide and complex ensembles numbered 22,000 each. A higher sampling rate was used for the previously computationally predicted Peptides IV, V, and VI and the other positive control, peptide III. 5000 peptide structures were predicted for each sequence, 5000 docked complexes were generated per docking run, and the final peptide and complex ensembles still numbered 22,000 each.

b

The two ranking orders (1’–5’ and 1–4) correspond to the different sampling rates used.