Free Energy Method Set 1 (Stage 2) -

Grand Challenge 2

Free Energy Set 1 (Stage 2) - Kendall's Tau

Free Energy Set 1 (Stage 2) - RMSEc

Submission ID Group/PI name Submitter Name Number of ligands Kendalls Tau Kendalls Tau Error RMSEc (kcal/mol) RMSEc Uncertainty Protocol Name from Protocol File List of Software Packages Used Full FE Method?
07tpe Julien Michel Julien Michel 15 0.04 0.18 3.76 1.40 alchemical free energy protocol with average network analysis FESetup, NetworkX Free energy
2612s Ulf Ryde, Alfonso Garcia-Sosa Martin Olsson 15 0.02 0.20 1.51 0.29 amber pmemd free energy perturbation with charge correction Amber Free energy
3idpo Carlos Camacho Bentley Wingert 15 0.14 0.20 0.95 0.16 quasi-exact Quasi-exact method Structure-based scoring
4botu Julien Michel Julien Michel 14 0.16 0.15 2.38 0.45 alchemical free energy protocol with average network analysis using same charge compounds and partial charge scaling FESetup, NetworkX Free energy
b2xt3 Merck Yuan Hu 15 0.14 0.20 4.99 0.74 MMGBSA ranking from 20 MD replicates MMGBSA Structure-based scoring
bqhi0 Xiaoqin Zou Xiaoqin Zou 15 0.16 0.20 0.96 0.13 MMGBSA MMGBSA Structure-based scoring
ck8kc     15 0.00 0.21 1.48 0.27 free energy perturbation with schrÉ_dinger fep/rest Schrodinger-FEP Free energy
e2nsc     15 0.08 0.19 6.51 0.95 Prime MMGBSA ranking for 102 set MMGBSA Structure-based scoring
eexcx Wei Yang Wei Yang 15 0.06 0.19 2.24 0.59 Orthogonal Space Sampling Based Free Energy Perturbation CHARMM Free energy
eta0e     15 0.31 0.17 6.93 1.81 QMMM ranking for FEP set QMMM Structure-based scoring
g18vf Merck Yuan Hu 15 0.08 0.16 5.70 0.93 MMGBSA ranking from 20 MD replicates MMGBSA Structure-based scoring
gzx7q     15 0.12 0.19 11.10 4.65 QMMM ranking for FEP set QMMM Structure-based scoring
inspj Julien Michel Julien Michel 15 0.12 0.13 2.39 0.42 alchemical free energy protocol with average network analysis FESetup, NetworkX Free energy
lh0zq Wei Yang Wei Yang 15 -0.14 0.21 1.86 0.37 Orthogonal Space Sampling Based Free Energy Perturbation CHARMM Free energy
nszkx Bogdan Iorga Bogdan Iorga 13 0.25 0.17 2.36 0.57 Alchemical Free Energy Calculation Gromacs Free energy
olv52 Julien Michel Julien Michel 14 0.11 0.18 1.81 0.46 alchemical free energy protocol with average network analysis using same charge compounds FESetup, NetworkX Free energy
pyxiv Zoe Cournia Christina Athanasiou 15 0.17 0.19 1.52 0.25 Free energy perturbation calculations Schrodinger-FEP Free energy
qpv1a Xiaoqin Zou Xiaoqin Zou 15 0.06 0.20 1.29 0.26 MMPBSA MMPBSA Structure-based scoring
t7htp     15 -0.12 0.20 99.70 26.60 Total Energy Total Energy Structure-based scoring
veadz     15 -0.06 0.23 18.20 2.55 IC50 conversion SeeSAR/HYDE Structure-based scoring
zkx4x Charles L. Brooks III Xinqiang Ding 15 -0.04 0.19 2.00 0.34 multi site lambda dynamics CHARMM Free energy
0aggj Guowei Wei Duc Nguyen 15 0.31 0.18 0.72 0.21 RI-Score RI-Score Structure-based scoring
22juj Emilio Gallicchio Rajat Kumar Pal 15 -0.01 0.24 2.21 0.29 HSA/BEDAM/OPLS2005/AGBNP2 # Binding Energy Distribution and Analysis Method # Analytical Generalized Born Non-Polar Model # Hydration Site Analysis BEDAM (Binding Energy Distribution Analysis Method) Structure-based scoring
327r0 Emilio Gallicchio Rajat Kumar Pal 15 -0.02 0.24 1.96 0.27 BEDAM/OPLS2005/AGBNP2 # Binding Energy Distribution and Analysis Method # Analytic Generalized Born Non-Polar Model BEDAM (Binding Energy Distribution Analysis Method) Structure-based scoring
4rbjk Guowei Wei Duc Nguyen 15 0.41 0.18 0.66 0.22 RI-Score RI-Score Structure-based scoring
66nbk Enrico Purisima Enrico Purisima 15 0.02 0.19 1.47 0.28 SIE + FiSH SIE (solvated interaction energy) with FISH solvation model Structure-based scoring
6mjkt David Evans Matthew Baumgartner 15 0.16 0.20 1.24 0.16 align_close_2 Smina Structure-based scoring
6nrpf David Koes David Koes 15 0.19 0.24 1.03 0.18 stage2_vinardo_score Vinardo Score Structure-based scoring
7wx7v Alexander D MacKerell Jr. Sirish Lakkaraju 15 0.19 0.17 2.09 0.38 SILCS-MC SILCS (Site Identification by Ligand Competitive Saturation) Structure-based scoring
86ozh Guowei Wei Duc Nguyen 15 0.19 0.20 0.75 0.23 RI-Score RI-Score Structure-based scoring
bw4pj Guowei Wei Duc Nguyen 15 0.34 0.18 0.67 0.21 RI-Score RI-Score Structure-based scoring
erdfw Xiaoqin Zou Xiaoqin Zou 15 0.06 0.20 1.29 0.26 MMPBSA MMPBSA Structure-based scoring
fww4f Garland R. Marshall Flavio Ballante 15 -0.30 0.22 1.09 0.33 FBRHGRM Method 2 AutoDock Vina, Clusterizer & DockAccessor Structure-based scoring
g4bd3 Andrey Voronkov Andrey Voronkov 15 -0.06 0.22 1.59 0.24 Vina-Smina method 1 Smina, dkoes scoring function Structure-based scoring
gia3u Alexander D MacKerell Jr. Sirish Lakkaraju 15 0.13 0.20 0.74 0.23 SILCS-MC SILCS (Site Identification by Ligand Competitive Saturation) Structure-based scoring
hj31e David Evans Matthew Baumgartner 15 -0.25 0.19 0.72 0.21 lly_ic50_svm In-house QSAR script Ligand-based scoring
jdr8n Xiaoqin Zou Xiaoqin Zou 15 0.16 0.20 0.96 0.13 MMGBSA MMGBSA Structure-based scoring
jtsy2 Guowei Wei Duc Nguyen 15 0.32 0.19 0.69 0.20 RI-Score RI-Score Structure-based scoring
li83b Max Totrov Maxim Totrov 15 0.25 0.20 0.57 0.14 ICM/APF 3D QSAR + MMGBSA Molsoft ICM Structure-based scoring
ljdjm     15 -0.16 0.19 1.15 0.24 glide_ensemble_docking Glide-XP Structure-based scoring
mbbz2 Andrey Voronkov Andrey Voronkov 15 -0.08 0.16 3.04 0.83 Vina-Smina method 2 Smina, Vinardo scoring function Structure-based scoring
moii1 Guowei Wei Duc Nguyen 15 0.16 0.20 0.68 0.19 RI-Score RI-Score Structure-based scoring
mtbxd Guowei Wei Duc Nguyen 15 -0.06 0.19 0.77 0.23 RI-Score RI-Score Structure-based scoring
n55eq Guowei Wei Duc Nguyen 15 0.33 0.19 0.74 0.23 RI-Score RI-Score Structure-based scoring
p8rak Max Totrov Maxim Totrov 15 0.25 0.20 0.57 0.14 ICM/APF 3D QSAR + MMGBSA MMGBSA_modified Structure-based scoring
rtqum Guowei Wei Duc Nguyen 15 0.25 0.20 0.71 0.25 RI-Score RI-Score Structure-based scoring
rwmcz Alexander D MacKerell Jr. Sirish Lakkaraju 15 0.14 0.20 0.68 0.22 SILCS-MC SILCS (Site Identification by Ligand Competitive Saturation) Structure-based scoring
sge2j Charles L. Brooks III Xinqiang Ding 15 0.06 0.20 0.96 0.28 Autodock Vina scoring based on conformations from flexible CDOCKER. AutoDock Vina Structure-based scoring
ska85     15 -0.02 0.21 14.32 1.91 Prime MMGBSA ranking for 102 set MMGBSA Structure-based scoring
vbzci Steve Jones Oleksandr Yakovenko 15 0.09 0.18 0.81 0.23 LIE with bootstrapping LIE (Linear Interaction Energy Model) Structure-based scoring
vovuk David Evans Matthew Baumgartner 15 -0.14 0.25 10.72 1.81 align_close_mmgbsa MMGBSA Structure-based scoring
vxvhq Stefano Moro Stefano Moro 15 0.21 0.20 6.24 1.31 MMS DockBench CrossDocking - MMGBSA Method MMGBSA Structure-based scoring
w8p2f Guowei Wei Duc Nguyen 15 0.16 0.20 0.72 0.23 RI-Score RI-Score Structure-based scoring
wfe3c David Koes David Koes 15 0.17 0.23 0.69 0.13 stage2_vina_score Vina Structure-based scoring
x8jt0     0 nan nan nan nan eTOX ALLIES eTOX ALLIES Structure-based scoring
xv7qs Enrico Purisima Enrico Purisima 15 0.04 0.18 0.86 0.15 SIE Method 1 SIE (solvated interaction energy) Structure-based scoring