1 research outputs found
CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge
Community
Structure–Activity Resource (CSAR) conducted a benchmark exercise
to evaluate the current computational methods for protein design,
ligand docking, and scoring/ranking. The exercise consisted of three
phases. The first phase required the participants to identify and
rank order which designed sequences were able to bind the small molecule
digoxigenin. The second phase challenged the community to select a
near-native pose of digoxigenin from a set of decoy poses for two
of the designed proteins. The third phase investigated the ability
of current methods to rank/score the binding affinity of 10 related
steroids to one of the designed proteins (p<i>K</i><sub>d</sub> = 4.1 to 6.7). We found that 11 of 13 groups
were able to correctly select the sequence that bound digoxigenin,
with most groups providing the correct three-dimensional structure
for the backbone of the protein as well as all atoms of the active-site
residues. Eleven of the 14 groups were able to select the appropriate
pose from a set of plausible decoy poses. The ability to predict absolute
binding affinities is still a difficult task, as 8 of 14 groups were
able to correlate scores to affinity (Pearson-<i>r</i> >
0.7) of the designed protein for congeneric steroids and only 5 of
14 groups were able to correlate the ranks of the 10 related ligands
(Spearman-ρ > 0.7)