Free Energy Method Set 2 (Stage 2) -

Grand Challenge 2

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

Free Energy Set 2 (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?
14qhp Xiaoqin Zou Xiaoqin Zou 18 0.24 0.17 1.56 0.21 MMPBSA MMPBSA Structure-based scoring
2etlu     18 0.11 0.15 7.72 1.03 Prime MMGBSA ranking for 102 set MMGBSA Structure-based scoring
2ytv8 Bogdan Iorga Bogdan Iorga 18 -0.15 0.23 4.37 1.35 Alchemical Free Energy Calculation Gromacs Free energy
4pnzi Xiaoqin Zou Xiaoqin Zou 18 0.18 0.18 1.49 0.22 MMGBSA MMGBSA Structure-based scoring
67a3e     18 0.53 0.15 73.50 8.07 Total Energy Total Energy Structure-based scoring
81n55     18 0.55 0.12 1.31 0.20 free energy perturbation with schrÉ_dinger fep/rest Schrodinger-FEP Free energy
aau3q     18 -0.17 0.18 24.30 4.50 QMMM ranking for FEP set QMMM Structure-based scoring
adxx8 Ulf Ryde, Alfonso Garcia-Sosa Martin Olsson 18 0.48 0.13 1.46 0.20 amber pmemd free energy perturbation with charge correction Amber Free energy
bdcdh Merck Yuan Hu 18 0.24 0.22 3.27 0.76 MMGBSA ranking from 20 MD replicates MMGBSA Structure-based scoring
d8fcq     18 0.37 0.16 2.56 0.48 QMMM ranking for FEP set QMMM Structure-based scoring
izhdb Charles L. Brooks III Xinqiang Ding 18 0.28 0.17 1.61 0.28 multi site lambda dynamics CHARMM Free energy
jzrt5 Julien Michel Julien Michel 18 0.37 0.14 1.45 0.23 alchemical free energy protocol with average network analysis and mixed scaling of partial charges FESetup, NetworkX Free energy
k32u2 Carlos Camacho Bentley Wingert 18 0.18 0.18 1.47 0.17 quasi-exact Quasi-exact method Structure-based scoring
qt771 Julien Michel Julien Michel 18 -0.14 0.20 4.11 0.74 alchemical free energy protocol with average network analysis FESetup, NetworkX Free energy
rvm67 Carlos Camacho Bentley Wingert 18 0.26 0.18 1.39 0.17 quasi-exact Quasi-exact method Structure-based scoring
szjdn Merck Yuan Hu 18 0.28 0.17 3.58 0.90 MMGBSA ranking from 20 MD replicates MMGBSA Structure-based scoring
x2j7p Zoe Cournia Christina Athanasiou 18 0.50 0.10 1.49 0.19 Free energy perturbation calculations Schrodinger-FEP Free energy
x7ib3     18 0.34 0.17 27.70 4.65 IC50 conversion SeeSAR/HYDE Structure-based scoring
xk67c Steve Jones Oleksandr Yakovenko 18 0.62 0.12 0.94 0.15 Jarzinsky umbrella sampling, fset0 Jarzinsky umbrella sampling Free energy
0aggj Guowei Wei Duc Nguyen 18 0.36 0.18 1.37 0.19 RI-Score RI-Score Structure-based scoring
22juj Emilio Gallicchio Rajat Kumar Pal 18 0.25 0.14 2.32 0.40 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 18 0.01 0.16 2.40 0.38 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 18 0.24 0.17 1.40 0.17 RI-Score RI-Score Structure-based scoring
66nbk Enrico Purisima Enrico Purisima 18 0.36 0.18 1.36 0.28 SIE + FiSH SIE (solvated interaction energy) with FISH solvation model Structure-based scoring
6mjkt David Evans Matthew Baumgartner 18 0.45 0.14 1.26 0.17 align_close_2 Smina Structure-based scoring
6nrpf David Koes David Koes 18 0.16 0.21 1.59 0.22 stage2_vinardo_score Vinardo Score Structure-based scoring
7wx7v Alexander D MacKerell Jr. Sirish Lakkaraju 18 0.42 0.16 1.34 0.19 SILCS-MC SILCS (Site Identification by Ligand Competitive Saturation) Structure-based scoring
86ozh Guowei Wei Duc Nguyen 18 0.35 0.16 1.30 0.17 RI-Score RI-Score Structure-based scoring
bw4pj Guowei Wei Duc Nguyen 18 0.09 0.16 1.46 0.20 RI-Score RI-Score Structure-based scoring
erdfw Xiaoqin Zou Xiaoqin Zou 18 0.24 0.17 1.56 0.21 MMPBSA MMPBSA Structure-based scoring
fww4f Garland R. Marshall Flavio Ballante 18 0.43 0.18 1.23 0.20 FBRHGRM Method 2 AutoDock Vina, Clusterizer & DockAccessor Structure-based scoring
g4bd3 Andrey Voronkov Andrey Voronkov 18 0.41 0.15 1.24 0.19 Vina-Smina method 1 Smina, dkoes scoring function Structure-based scoring
gia3u Alexander D MacKerell Jr. Sirish Lakkaraju 18 -0.25 0.19 1.53 0.19 SILCS-MC SILCS (Site Identification by Ligand Competitive Saturation) Structure-based scoring
hj31e David Evans Matthew Baumgartner 18 -0.56 0.17 1.55 0.20 lly_ic50_svm In-house QSAR script Ligand-based scoring
jdr8n Xiaoqin Zou Xiaoqin Zou 18 0.18 0.18 1.49 0.22 MMGBSA MMGBSA Structure-based scoring
jtsy2 Guowei Wei Duc Nguyen 18 0.13 0.18 1.49 0.20 RI-Score RI-Score Structure-based scoring
li83b Max Totrov Maxim Totrov 18 0.40 0.14 1.22 0.17 ICM/APF 3D QSAR + MMGBSA Molsoft ICM Structure-based scoring
ljdjm     18 0.53 0.12 1.10 0.16 glide_ensemble_docking Glide-XP Structure-based scoring
mbbz2 Andrey Voronkov Andrey Voronkov 18 0.28 0.14 1.67 0.22 Vina-Smina method 2 Smina, Vinardo scoring function Structure-based scoring
moii1 Guowei Wei Duc Nguyen 18 0.09 0.16 1.48 0.19 RI-Score RI-Score Structure-based scoring
mtbxd Guowei Wei Duc Nguyen 18 0.40 0.16 1.34 0.19 RI-Score RI-Score Structure-based scoring
n55eq Guowei Wei Duc Nguyen 18 0.28 0.18 1.37 0.17 RI-Score RI-Score Structure-based scoring
p8rak Max Totrov Maxim Totrov 18 0.40 0.14 1.22 0.17 ICM/APF 3D QSAR + MMGBSA MMGBSA_modified Structure-based scoring
rtqum Guowei Wei Duc Nguyen 18 0.44 0.14 1.29 0.17 RI-Score RI-Score Structure-based scoring
rwmcz Alexander D MacKerell Jr. Sirish Lakkaraju 18 0.14 0.17 1.48 0.19 SILCS-MC SILCS (Site Identification by Ligand Competitive Saturation) Structure-based scoring
sge2j Charles L. Brooks III Xinqiang Ding 18 0.44 0.14 1.34 0.22 Autodock Vina scoring based on conformations from flexible CDOCKER. AutoDock Vina Structure-based scoring
ska85     18 0.00 0.19 14.04 2.34 Prime MMGBSA ranking for 102 set MMGBSA Structure-based scoring
vbzci Steve Jones Oleksandr Yakovenko 18 0.32 0.17 1.18 0.15 LIE with bootstrapping LIE (Linear Interaction Energy Model) Structure-based scoring
vovuk David Evans Matthew Baumgartner 18 0.45 0.14 13.45 1.72 align_close_mmgbsa MMGBSA Structure-based scoring
vxvhq Stefano Moro Stefano Moro 18 0.30 0.16 2.50 0.37 MMS DockBench CrossDocking - MMGBSA Method MMGBSA Structure-based scoring
w8p2f Guowei Wei Duc Nguyen 18 0.29 0.16 1.39 0.18 RI-Score RI-Score Structure-based scoring
wfe3c David Koes David Koes 18 0.24 0.20 1.65 0.30 stage2_vina_score Vina Structure-based scoring
xv7qs Enrico Purisima Enrico Purisima 18 0.17 0.18 1.44 0.23 SIE Method 1 SIE (solvated interaction energy) Structure-based scoring