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 |