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. Author manuscript; available in PMC: 2019 Jan 1.
Published in final edited form as: J Comput Aided Mol Des. 2017 Dec 4;32(1):1–20. doi: 10.1007/s10822-017-0088-4

Table 4.

Top 10 submissions in terms of RMSEc, in order of increasing RMSEc, for the two free energy sets in both stages of the challenge. Error bars are illustrated in Fig. 5 and listed in Tables S7–S12. Methods include predictions from scoring methods with free energy estimates in the affinity ranking component of the challenge, and free energy methods in the free energy component of the challenge. Methods in bold are common methods submitted by the same participant across FE sets.

Stage 1
FE Set 1
RMSEc Software Used Submitter Name Group/PI Name Receipt ID
0.66 CDOCKER (pose prediction) + Autodock Vina (scoring) Xinqiang Ding Charles L. Brooks III pgbuh
0.68 In-house machine learning score Anonymous Anonymous c0l1t
0.68 In-house machine learning score Anonymous Anonymous 5bvwx
0.69 SILCS approximate FE method Sirish Lakkaraju Alexander D MacKerell Jr. 2umsq
0.70 Vina doha naga In silico Drug Design Master 1bhkb
0.70 Vina Olivier Bequignon In silico Drug Design Master 2yqgz
0.70 AutoDock Vina doha naga In silico Drug Design Master 87x7c
0.70 AutoDock Vina Olivier Bequignon In silico Drug Design Master g7q2q
0.75 In-house machine learning score Anonymous Anonymous xr834
0.75 In-house machine learning score Anonymous Anonymous dnil6
FE Set 2
RMSEc Software Used Submitter Name Group/PI Name Receipt ID
0.98 FESetup (Automating Setup for Alchemical Free Energy Simulations) with average network analysis Julien Michel Julien Michel f6een
1.07 Smina Matthew Baumgartner David Evans gzd7a
1.18 AutoDock Vina doha naga In silico Drug Design Master 87x7c
1.18 AutoDock Vina Olivier Bequignon In silico Drug Design Master g7q2q
1.18 Vina Olivier Bequignon In silico Drug Design Master 5nsef
1.18 Vina doha naga In silico Drug Design Master eg8rg
1.25 Quasi exact method FE method Bentley Wingert Carlos Camacho 2efa1
1.35 LIE (Linear Interaction Energy Model) Oleksandr Yakovenko Steve Jones l8rmr
1.36 MCPro (Monte Carlo free energy perturbation) Zhaoping Xiong Mingyue Zheng sndmm
1.36 Glide-XP Zhaoping Xiong Mingyue Zheng lpcmd
Stage 2
FE Set 1
RMSEc Software Used Submitter Name Group/PI Name Receipt ID
0.57 Trained MMGB/SA Maxim Totrov Max Totrov p8rak
0.57 Trained 3D QSAR + MMGB/SA Maxim Totrov Max Totrov li83b
0.66 Trained Random Forest Model, Rl-score Anonymous Anonymous 4rbjk
0.67 Trained Random Forest Model, Rl-score Anonymous Anonymous bw4pj
0.68 Trained Random Forest Model, Rl-score Anonymous Anonymous moii1
0.68 SILCS approximate FE method Sirish Lakkaraju Alexander D MacKerell Jr. rwmcz
0.69 Vina David Koes David Koes wfe3c
0.69 Trained Random Forest Model, Rl-score Anonymous Anonymous jtsy2
0.71 Trained Random Forest Model, Rl-score Anonymous Anonymous rtqum
0.72 QSAR Method Matthew Baumgartner David Evans hj31e
FE Set 2
RMSEc Software Used Submitter Name Group/PI Name Receipt ID
0.94 Explicit solvent FE (Jarzynski pulling) Oleksandr Yakovenko Steve Jones xk67c
1.10 Glide ensemble docking to known structure Anonymous Anonymous ljdjm
1.19 Trained Linear Interaction Energy Model Oleksandr Yakovenko Steve Jones vbzci
1.22 Trained 3D QSAR + MMGB/SA Maxim Totrov Max Totrov li83b
1.22 Trained MMGB/SA Maxim Totrov Max Totrov p8rak
1.23 AutoDock Vina with overlay docking Flavio Ballante Garland R. Marshall fww4f
1.24 Smina + in-house scoring function Andrey Voronkov Andrey Voronkov g4bd3
1.26 Smina Matthew Baumgartner David Evans 6mjkt
1.29 FESetup (Automating Setup for Alchemical Free Energy Simulations) with average network analysis Julien Michel Julien Michel c1nbt
1.30 Trained Random Forest Model, Rl-score Anonymous Anonymous rtqum