Grand Challenge 2

Pose RMSDs (Å) - Compound: AVG - Pose 1

Compound:
Submission ID Group/PI name Submitter Name Number of ligands Median RMSD (Å) Mean RMSD (Å) Standard Deviation of RMSD Protocol Name from Protocol File List of Software Packages Used
02sil     35 4.33 4.33 3.38 ProPKA/Obabel/VINA/AutoDock/SeeSAR Method 1 AutoDock 4, SeeSAR (minimization), HYDE scoring function, Visual
0lxp5 Soderhjelm Research Group P_r S_derhjelm 35 4.70 4.54 3.14 Multi-target Docking using Autodock Vina AutoDock Vina
0xk7w David Koes David Koes 35 5.98 5.07 2.62 cnn_combined Smina, gnina-cnn (rescoring, trained using CSAR and virtual screening data from DUDE)
3rfl5 Xiaoqin Zou Xiaoqin Zou 35 3.74 4.30 3.45 A hierarchical docking method, XDZ_5 OMEGA (LigConfSampling),SHAFTS (structral similarity score), AutoDock Vina (pose sampling), ITScore_v2_TF (knowledge-based scoring function)
3rj71 Mingyue Zheng Zhaoping Xiong 35 5.90 6.34 1.64 Glide OMEGA (LigConfSampling), AutoDock Vina
4i2mb Xiaoqin Zou Xiaoqin Zou 35 1.75 3.79 3.32 A hierarchical docking method, XDZ_4 OMEGA (LigConfSampling),SHAFTS (structral similarity score), AutoDock Vina (pose sampling), ITScore_v2_TF (knowledge-based scoring function)
5cf33 Garland R. Marshall Flavio Ballante 35 1.20 2.76 3.04 FBRHGRM Method 1 Modeller, Gromacs (minimization), surflex-sim, Clusterizer and DockAccessor, Vina
5rqrx Kam Y.J. Zhang Ashutosh Kumar 35 1.19 2.92 2.94 CDVS ROCS, Omega, Glide-SP-XP
6tnqb Carlos Camacho Bentley Wingert 35 2.25 3.43 3.10 dock_close Smina, visual
7ltmc Merck Yuan Hu 35 1.02 2.19 2.48 MMGBSA Pose Prediction from 20 replicates of molecular dynamics simulations GLIDE-CCDC-GOLD, Amber14, MMGBSA
7rmfb Ho Leung Ng Ho Leung Ng 35 5.78 5.13 2.68 ERF-DOCK Smina, idock-RF-v3, Yasara (simulated annealing), visual
8mocv Southwest Research Institute Jonathan Bohmann 35 7.53 11.87 8.40 Rhodium HTS Mode Rhodium380E6-4 (propietary)
am6an Alfonso T. Garcia-Sosa Alfonso T. Garcia-Sosa 35 3.28 4.17 2.93 qpld_XP_vina Schrodinger QM-polarized ligand docking, Glide XP, AutoDock Vina
byf51 Soderhjelm Research Group P_r S_derhjelm 35 4.57 4.25 2.80 MD refinement of docking poses AutoDock Vina, Gromacs
cfn8u     35 1.16 2.37 2.43 glide_ensemble_docking Glide-XP
clzrj     35 6.96 6.75 1.88 Smina/RF-Score-VS v2 Smina, RF-Score-VS v2 and v3
e0aar     35 6.94 6.03 2.49 Maestro/Gold/Tscore CCDC-Gold, In-house machine learning scoring
elm2r Grudinin Sergei Grudinin 35 1.91 3.65 3.20 Convex-PL AutoDock Vina, Convex-PL scoring function
gdhv4 Xiaoqin Zou Xiaoqin Zou 35 1.80 4.12 3.54 A hierarchical docking method, XDZ_2 OMEGA (LigConfSampling),SHAFTS (structral similarity score), AutoDock Vina (pose sampling), ITScore_v1 (knowledge-based scoring function)
gfifa Stefano Moro Stefano Moro 35 1.75 3.92 3.89 MMS DockBench CrossDocking Method 1 ROCS TanimotoComboShapeSimilarity, DockBench: autodock-ga,autodock-lga,autodock-ls,glide-sp,gold-asp,gold-chemscore,gold-goldscore,gold-plp,moe-affinitydg,moe-gbviwsa,moe-londondg,plants-chemplp,plants-plp,plants-plp95,rdock-solv,rdock-std
h67ea Carlos Camacho Bentley Wingert 35 2.25 3.43 3.10 dock_close Smina, visual
hciq4 Merck Hongwu Wang 35 1.13 2.19 2.39 Visual inspection Glide, Gold, Induced-fit-docking
ixnzu Max Totrov Maxim Totrov 35 1.17 1.95 2.24 ICM Dock Molsoft ICM
jz0em Enrico Purisima Enrico Purisima 35 1.39 2.27 2.46 Wilma/SIE Method 1 Wilma (flexible ligand docking algorithm), scoring function SIE (force field based scoring function)
knz3v Stefano Moro Stefano Moro 35 7.02 7.67 4.77 MMS CrossDocking - Protein APO (PAPO) Method 2 Cross-Docking Benchmark, Gold-goldscore
l835g Soderhjelm Research Group P_r S_derhjelm 35 4.73 4.39 2.79 Reconnaissance metadynamics and MD refinement of docking poses AutoDock Vina, Gromacs, Reconnaissance metadynamic (enhanced sampling)
mgxbc Xiaoqin Zou Xiaoqin Zou 35 1.00 2.76 2.84 A template-based method, XDZ_0 OMEGA, SHAFTS, NoDocking, Amber11
mmj0e Xiaoqin Zou Xiaoqin Zou 35 1.80 3.77 3.13 A hierarchical docking method, XDZ_1 OMEGA (LigConfSampling),SHAFTS (structral similarity score), AutoDock Vina (pose sampling), ITScore_TF (knowledge-based scoring function)
mx1v2 David Koes David Koes 35 6.09 5.28 3.22 cnn_csar_fxr Smina, gnina-cnn (rescoring, trained using CSAR and FXR ligand poses from PDB)
oky3v Zoe Cournia Christina Athanasiou 35 0.99 2.34 2.62 Physics-based pose predictions guided by native ligands WaterMap, SHAPE Screening, Structural Interaction Fingerprint, DFT/B3LYP/6-31G*, GLIDE-SP-XP, Induced-fit-docking, Emodel/GlideScore-SP, Binding Pose Metadynamics
piwlh David Evans Matthew Baumgartner 35 2.07 3.48 2.82 ifd_ens Induced-fit-docking
psiuj David Evans Matthew Baumgartner 35 1.20 3.16 3.10 manual Forge, Smina (minimization only), Visual inspection, Glide-SP
qbvvg Xiaoqin Zou Xiaoqin Zou 35 1.75 3.26 2.98 A hierarchical docking method, XDZ_3 OMEGA (LigConfSampling),SHAFTS (structral similarity score), AutoDock Vina (pose sampling), ITScore_v1_TF (knowledge-based scoring function)
qfrw4 Charles L. Brooks III Xinqiang Ding 35 1.59 3.44 3.73 Docking using CDOCKER from CHARMM plus Scoring using AutoDock Vina Simulated Annealing, CDOCKER, Vina (rescored)
qfu33 David Evans Matthew Baumgartner 35 1.79 3.32 2.84 metad_ens Induced-fit-docking, Binding pose metadynamics (rescoring)
qt334 David Koes David Koes 35 6.60 6.34 2.49 cnn_csar Smina, gnina-cnn (rescoring, trained using CSAR)
qxrku Alexandre Bonvin Alexandre Bonvin 35 6.39 6.15 1.71 HADDOCK2.2 protein-ligand protocol HADDOCK2.2
tbuot Didier Rognan Didier ROGNAN 35 2.69 3.38 2.53 Surflex/GRIM Interaction Pattern Similarity/ HYDE (Protocol 2) Surflex, Ichem-GRIM (InteractionPatternSim), HYDE
to4tt David Koes David Koes 35 1.75 3.53 2.91 vina Smina
txyzj Steve Jones Oleksandr Yakovenko 35 1.27 2.12 1.93 AI_MD Autodock Vina, GROMACS, in-house LIE (Linear Interaction Energy Model)
utpcl Didier Rognan Didier ROGNAN 35 1.94 3.26 2.72 Surflex/GRIM Interaction Pattern Similarity/ HYDE (Protocol3) Surflex, Ichem-GRIM (InteractionPatternSim), HYDE
wax1j David Evans Matthew Baumgartner 35 1.20 3.08 3.13 align_close MOE (most-similar-mol), Confgen, Forge (alignment), Smina (minimization), Manual ranking
wzu5m     35 1.41 3.13 3.07 Glide/Gold/xScore Glide, CCDC Gold, Xscore (rescored)
x7jp3 David Evans Matthew Baumgartner 35 1.63 3.79 3.47 smina_ens Smina
ypz46     35 7.28 6.24 3.60 Smina/RF-Score-VS v3 Smina, RF-Score-VS v2 and v3
yyjmb Rognan, Didier Didier ROGNAN 35 2.08 3.59 2.93 Surflex/GRIM Interaction Pattern Similarity/ HYDE(Protocol 1) Surflex, Ichem-GRIM (InteractionPatternSim), HYDE