Skip to main content
. Author manuscript; available in PMC: 2021 Feb 1.
Published in final edited form as: J Comput Aided Mol Des. 2019 Nov 16;34(2):131–147. doi: 10.1007/s10822-019-00237-5

Table 1:

Overview of MathDL’s performance in D3R GC4. The numbers in “(a/b)” indicates that a number of our predictions had the ranking and there was a total of b submissions sharing the ranking.

Dataset Contest Results
Pose Prediction
BACE Stage 1A Pose Prediction Ranked 1st (1/2)i; Ranked 2nd (3/3)ii
BACE Stage 1B Pose Prediction Ranked 2nd (2/2)iii; Ranked 3rd (1/2)iv
Affinity Predictions
Cathepsin Stage 2 Combined Ligand and Structure Based Scoring Ranked 1st (2/5)v; Ranked 2nd (2/3)vi; Ranked 3rd (2/4)vii
Cathepsin Stage 2 Ligand Based Scoring No participation
Cathepsin Stage 2 Structure Based Scoring Ranked 1st (2/4)viii; Ranked 2nd (3/3)ix; Ranked 3rd(3/3)x
Cathepsin Stage 2 Free Energy Set Ranked 1st (1/7)xi; Ranked 2nd (1/7)xii; Ranked 3rd(3/5)xiii
BACE Stage 1 Combined Ligand and Structure No participation
BACE Stage 1 Ligand Based Scoring No participation
BACE Stage 1 Structure Based Scoring No participation
BACE Stage 1 Free Energy Set No participation
BACE Stage 2 Combined Ligand and Structure
BACE Stage 2 Ligand Based Scoring No participation
BACE Stage 2 Structure Based Scoring
BACE Stage 2 Free Energy Set Ranked 2nd (3/4)xiv; Ranked 3rd (1/4)xv
Superscript Submission ID Evaluation Metric Docking Protocol Scoring Protocol
i 5t302 Median RMSD DM1
ii 5t302 Mean RMSD DM1
0invp Median RMSD DM4
0invp Mean RMSD DM4
iii 2ieqo Median RMSD DM4
itzv6 Mean RMSD DM3
iv 4myne Mean RMSD DM1
v 0xvrb Spearman’s ρ DM3 BP2
3c8nw Spearman’s ρ DM4 BP2
vi 0xvrb Kendall’s τ DM3 BP2
3c8nw Kendall’s τ DM4 BP2
vii qb2s2 Kendall’s τ DM1 BP2
qb2s2 Spearman’s ρ DM1 BP2
viii 0xvrb Spearman’s ρ DM3 BP2
3c8nw Spearman’s ρ DM4 BP2
ix 0xvrb Kendall’s τ DM3 BP2
3c8nw Kendall’s τ DM4 BP2
qb2s2 Spearman’s ρ DM1 BP2
x qb2s2 Kendall’s τ DM1 BP2
qi5ev Spearman’s ρ DM3 BP1
kohoc Spearman’s ρ DM2 BP2
xi ar5p6 RMSEc DM4 BP2
xii 24b03 RMSEc DM3 BP2
xiii 24b03 Kendall’s τ DM3 BP2
24b03 Spearman’s ρ DM3 BP2
24b03 Pearson’s r DM3 BP2
xiv 8frur Kendall’s τ DM1 BP2
8frur Spearman’s ρ DM1 BP2
8frur RMSEc DM1 BP2
xv 8frur Pearson’s r DM1 BP2