Grand Challenge 4 - Pose Prediction Method - BACE (Stage 1A)

Pose RMSDs (Å) - Pose 1

Compound:

Receipt ID Submitter Name PI/Group Name Number of Ligands Median RMSD Mean RMSD STD RMSD Method Name Software
0cdix Antonia MeyJulien michel 20 7.9 6.92 4.92 flare_docking flare 2.0.0 revision 34140
0fgte Rodrigo QuirogaVillarreal marcos 20 3.63 5.53 4.28 2vinardo-beta rdkit / mgltools/ smina (modified)
0invp Kaifu GaoGuowei wei 20 0.53 0.8 0.59 deep learning assisted similarity docking efindsite 1.3, openbabel 2.4.1, discover studio visualizer 4.5, maestro 10.2, shafts, guassian 09, amber 16, homemade deep learning
0zdxk Bogdan IorgaBogdan iorga 20 0.81 1.48 2.12 d3r-gc4-pose-bestscore-phase-1a cactvs chemoinformatics toolkit v3.433/schr_dinger suite 2018-1/corina v3.60/ucsf chimera v1.10.2/gold v5.2
37v4p Bentley WingertCarlos camacho 20 1.25 1.31 0.57 dock close openbabel 2.3.2 maestro 2018-3 prime smina apr 2 2016
3i0ua Manon RauMatthieu montes 20 1.74 1.98 1.05 rdock_adt icon/chemaxon/rdock/autodock 4.2
4h67m Paul FrancoeurDavid koes 20 4.54 5.47 2.78 aligned autodock vina rdkit/gnina/smina
4x5a8 Dima KozakovDima kozakov 20 0.63 0.76 0.34 macrocycle align brikard, libmol , rdkit, openbabel,
54duu Cyril, nam, edouard Bigot, husain, mahieuUniversity paris diderot 20 2.48 5.66 4.69 knime/rdkit/chemaxon/mgltools/autodock vina knime/rdkit/chemaxon/mgltools/autodock vina
5iz88 Paul FrancoeurDavid koes 20 45.84 44.44 4.87 blind cnn rdkit/gnina/smina
5t302 Kaifu GaoGuowei wei 20 0.53 0.8 0.6 deep learning assisted similarity docking efindsite 1.3, openbabel 2.4.1, discover studio visualizer 4.5, maestro 10.2, shafts, guassian 09, amber 16, homemade deep learning
6gz2t Stefano ForliForli 20 1.28 1.28 0.33 autodock 4.x gpu with visual inspection autodock 4.x gpu
7yni2 Manon RauMatthieu montes 20 2.4 2.93 1.93 rdock_seesar icon/chemaxon/rdock/seesar
apue7 Attilio VargiuAttilio vittorio vargiu 20 3.1 4.83 3.5 haddock2.2 protein-ligand edes-based all hydrogen docking protocol haddock webserver 2.2 openeye omega 2018.feb.1 openeye shape 2018.feb.1 openeye rocs 3.2.2.2 chemminer 3.32.1 fmcsr 1.22
axtm4 Sukanya/lea Sasmal/el khouryDavid mobley 20 1.35 1.59 0.87 omega/hybrid/mm-gbsa omega 3.0.8/hybrid 3.2.0.2/mm-gbsa/amber16
biw3a Maria KadukovaSergei grudinin 20 1.67 1.87 0.98 multiple initial conformations with manual and ligand similarity based selection from the top-50 poses. autodock vina with in-house modifications, rdkit 2017, scipy, ligsif, pymol 1.8.4, unreleased version of convex-pl scoring function
bsrv5 Maria KadukovaSergei grudinin 20 2.5 2.73 1.88 multiple initial conformations re-scored by convex-pl with a regression model (solvent modeled with sasa and ncontacts) and automatically chosen by similarity. autodock vina with in-house modifications, rdkit 2017, scipy, pymol 1.8.4, unreleased version of convex-pl scoring function
buck5 Maria KadukovaSergei grudinin 20 3.51 4.15 3.05 multiple initial conformations re-scored by convex-pl with a regression model (solvent modeled with points on a grid). autodock vina with in-house modifications, rdkit 2017, scipy, pymol 1.8.4, unreleased version of convex-pl scoring function
ctr4g Paul FrancoeurDavid koes 20 46.55 46.38 1 blind autodock vina rdkit/gnina/smina
dg3gy Alexandre BonvinAlexandre bonvin 20 2.19 1.99 0.91 haddock2.2 protein-ligand refinement protocol haddock webserver 2.2 openeye omega 2018.feb.1 openeye shape 2018.feb.1 openeye rocs 3.2.2.2 chemminer 3.32.1 fmcsr 1.22
dxjg7 Ashutosh KumarKam zhang 20 1.05 1.23 0.66 popss-lite omega 3.0.0.1 rocs 3.2.2.2 glide 6.1
e2pw6 Par SoderhjelmSoderhjelm research group 20 5.14 5.72 3.35 multitarget/autodock_vina/pose&rank openbabel 2.4.0/vmd 1.9.2/pdb-tools (j. rodrigues)/mgltools/autodock tools 1.5.6/autodock vina 1.1.2/gromacs 2018/pose&rank web server (sali lab)
ecdg6 Bo WangHo-leung ng 20 3.17 13.92 20.54 semi-crossdocking with vinardo autodock-vina/smina-vinardo/fragfp-datawarrior/openbabel 2.4.1/openeye-omega
epvj2 Manon RauMatthieu montes 20 2.42 3.17 3.06 vina_rdock icon/chemaxon/mgltools/autodock vina/rdock
f4rwu Woong-hee ShinDaisuke kihara 20 8.75 7.71 2.96 docking pose rescoring using pl-patchsurfer autodock vina 1.1.2 pl-patchsurfer2
fky0k Polo LamMax totrov 20 0.69 0.92 0.46 icm dock with 4d receptor ensemble and apf ligand bias molsoft icm 3.8-7b
gd5eo Manon RauMatthieu montes 20 1.72 2.04 1.19 rdock_vina icon/chemaxon/rdock/vina
gduxh Manon RauMatthieu montes 20 2.2 2.34 1.53 vina_rdock_solv icon/chemaxon/mgltools/autodock vina/rdock_solv
gynvw Manon RauMatthieu montes 20 1.81 2.22 1.69 vina_vina icon/chemaxon/mgltools/autodock vina
i065y Sukanya/lea Sasmal/el khouryDavid mobley 20 1.83 1.87 0.71 omega/hybrid/mm-gbsa omega 3.0.8/hybrid 3.2.0.2/mm-gbsa/amber16
i82td Oleg StroganovBiomoltech inc. 20 1.4 1.51 0.65 lead finder + xedex conformer sampling lead finder 1808, xedex, build model 1808
isy26 Manon RauMatthieu montes 20 1.82 1.82 0.67 rdock_rdock icon/chemaxon/rdock
ix3cv Paul FrancoeurDavid koes 20 4.54 5.27 2.67 aligned cnn rdkit/gnina/smina
jit54 Maria KadukovaSergei grudinin 20 2.5 2.73 1.88 multiple initial conformations re-scored by convex-pl with a regression model (solvent modeled with points on a grid) and automatically chosen by similarity. autodock vina with in-house modifications, rdkit 2017, scipy, pymol 1.8.4, unreleased version of convex-pl scoring function
jpk87 Chao YangYingkai zhang 20 1.07 1.57 1.63 flexible-ligand docking protocol using rdkit generated low energy conformers smina (a fork of autodock vina) / rdkit (version 2018.03.2) / pdb2pqr (version 2.1.1) / autodocktools (version 1.5.6)
k03ed Chao YangYingkai zhang 20 1.06 1.15 0.34 flexible-ligand/ensemble receptor docking protocol smina (a fork of autodock vina) / rdkit (version 2018.03.2) / pdb2pqr (version 2.1.1) / autodocktools (version 1.5.6)
kmtri Attilio VargiuAttilio vittorio vargiu 20 3.12 4.21 2.73 haddock2.2 protein-ligand ensemble-docking protocol with enhanced-sampling of pocket shape haddock webserver 2.2 openeye omega 2018.feb.1 openeye shape 2018.feb.1 openeye rocs 3.2.2.2 chemminer 3.32.1 fmcsr 1.22
kvzm4 Ye ZouHo-leung ng 20 5.79 21.42 22.05 semi-crossdocking with vinardo and energy minimization. autodock-vina/smina-vinardo/fragfp-datawarrior/openbabel 2.4.1/openeye-omega/yasara
nwm5a Alexandre BonvinAlexandre bonvin 20 1.5 1.68 0.86 haddock2.2 protein-ligand flexible refinement protocol haddock webserver 2.2 openeye omega 2018.feb.1 openeye shape 2018.feb.1 openeye rocs 3.2.2.2 chemminer 3.32.1 fmcsr 1.22
oa8io Manon RauMatthieu montes 20 1.71 1.67 0.72 champion's_list icon/chemaxon/rdock/vina/seesar/autodock 4.2/rdock_solv
oen8j Manon RauMatthieu montes 20 1.85 1.92 0.71 rdock_rdock_solv icon/chemaxon/rdock/rdock_solv
ooptr Ashutosh KumarKam zhang 20 1.13 1.27 0.6 popss omega 3.0.0.1 rocs 3.2.2.2 rosetta suite 2015.25
pbt5s Cheng PengWeiliang zhu 20 3.22 3.48 2.31 2d-remd maestro gromacs 5.1.4 plumed 2.3.3
pe6zg Attilio VargiuAttilio vittorio vargiu 20 2.25 3.1 2.57 ensemble-docking with autodock4.2 and enhanced-sampling of pocket shape vmd 1.9.3 pymol 1.8.4 mgltools 1.5.6 amber18 gromacs2016.5 r3.5.1 plumed2.4 autodock4.2 openeye omega 2018.feb.1 openeye shape 2018.feb.1 openeye rocs 3.2.2.2 chemminer 3.32.1 fmcsr 1.22
q7ah7 Pin ChenChen Pin 20 6.48 7.02 2.77 pin chen schrodinger (glide tools) (2018-2 version) for docking,sitemap tools for binding sites predicting.
qjto3 Bentley WingertCarlos camacho 20 1.23 1.2 0.57 dock close manual openbabel 2.3.2 maestro 2018-3 prime smina apr 2 2016
qk28f Hasan h. InceHasan h. ince 20 8.86 13.76 9.51 drugitt docking protocol in-house
qqou3 Alejandro Varela rialGianni de fabritiis 20 0.87 1.24 0.61 skeledock htmd1.13.8/acemd2/rdkit2018.03.4
qz5tn Manon RauMatthieu montes 20 1.81 2.22 1.69 vina_adt icon/chemaxon/mgltools/autodock vina/autodock 4.2
rapwf Bogdan IorgaBogdan iorga 20 0.81 1.04 0.57 d3r-gc4-pose-bestpose-phase-1a cactvs chemoinformatics toolkit v3.433/schr_dinger suite 2018-1/corina v3.60/ucsf chimera v1.10.2/gold v5.2
rwov6    20 3.58 3.59 1.56 molecular similarity/ ligand alignment rdkit (2018.03.4) / moe (2018.0101) / swiss-model
s4fu0 Maria KadukovaSergei grudinin 20 4.94 5.7 3.27 multiple initial conformations re-scored by convex-pl. autodock vina with in-house modifications, rdkit 2017, scipy, pymol 1.8.4, unreleased version of convex-pl scoring function
sg870 Par SoderhjelmSoderhjelm research group 20 2.95 4.41 2.89 multitarget/autodock_vina openbabel 2.4.0/vmd 1.9.2/pdb-tools (j. rodrigues)/mgltools/autodock tools 1.5.6/autodock vina 1.1.2/gromacs 2018
shswj Stefano ForliForli 20 1.37 1.43 0.38 autodock 4.x gpu with substructure filters autodock4.x gpu/openbabel/python
skftb Manon RauMatthieu montes 20 11.96 11.27 2.58 vina_seesar icon/chemaxon/mgltools/autodock vina/seesar
t3ddc Xianjin XuXiaoqin zou 20 0.97 1.03 0.57 a hierarchical docking method xdz_1 maestro/openeye/mgltools/autodock vina
tm8kw Stefano ForliForli 20 1.95 2.38 1.56 autodock 4.x gpu autodock4.x gpu/openbabel/python
uf8ik Jamal ShamsaraJamal shamsara 20 10.26 9.56 2.14 pose prediction using flexx leadit 2.3.2/chem 3d 2016#
uq8b0    20 0.71 0.94 0.66 similarity/alignment/minimization rdkit/torch/macromodel
uqapi Benjamin BrownJens meiler 20 4.64 5.67 3.2 bclmolalign bcl v3.5, corina v4.1.0
wp8n0    20 2.35 2.43 0.69 ligand_shape_similarity_flexible_alignment autodock vina 1.1.2/rdkit 2018.03.1/openbabel/pymol/fkcombu
xdd3r Hahnbeom ParkInstitute for protein design 20 0.96 1.18 0.82 rosetta gadock rosetta (pre-release version, git hash 845e653c80ec0965c63afa747b6c7efde2ef63b8)/corina classic, webserver version/openbabel-2.4.1/antechamber-17.3
xgctb Benjamin BrownJens meiler 20 4.2 5.52 3.33 bclmolalign with protein-ligand complex energy minimization bcl v3.5, corina v4.1.0, moe 2018.01
xpien Jonathan BohmannMedicinal and process chemistry 20 3.82 4.23 1.6 ligandmatch ligandmatch 1.0 openbabel 2.3.90
xsm5f Alexandre BonvinAlexandre bonvin 20 2.68 4.72 3.72 haddock2.2 protein-ligand template-based docking protocol haddock webserver 2.2 openeye omega 2018.feb.1 openeye shape 2018.feb.1 openeye rocs 3.2.2.2 chemminer 3.32.1 fmcsr 1.22
ycvny    20 2.57 2.71 1.32 ligand_shape_similarity_vina_docking autodock vina 1.1.2/rdkit 2018.03.1/openbabel/pymol/fkcombu/acpype/gromacs 5.1.5
maej5 Maria KadukovaSergei grudinin 20 3.51 4.15 3.05 multiple initial conformations re-scored by convex-pl with a regression model (solvent modeled with sasa and ncontacts). autodock vina with in-house modifications, rdkit 2017, scipy, pymol 1.8.4, unreleased version of convex-pl scoring function
yw3a0 Carlos ModenuttiMarcelo marti 20 1.02 1.18 1.08 dockq moe2016.08/autodock4/mgltools1.5.7rc1/amber16/ligprep/rdkit2018-3
zav0x Ashutosh KumarKam zhang 20 1.05 1.18 0.54 popss-pb omega 3.0.0.1 rocs 3.2.2.2 szybki 1.9.0.3
zb4ps Cyril, nam, edouard Bigot, husain, mahieuUniversity paris diderot 20 4.84 4.88 1.65 knime/rdkit/chemaxon/mgltools/autodock vina knime/rdkit/chemaxon/mgltools/autodock vina
m7t0w Andre StanderDr andre stander 20 1.19 1.45 0.75 grambina grambina, amber, gromacs, chimera, rdkit
m0yfh Cyril, nam, edouard Bigot, husain, mahieuUniversity paris diderot 20 8.01 6.78 2.63 knime/rdkit/chemaxon/mgltools/autodock vina knime/rdkit/chemaxon/mgltools/autodock vina
nstab Attilio VargiuAttilio vittorio vargiu 20 1.78 2.86 2.71 ensemble-docking with autodock4.2 and enhanced-sampling of pocket shape and further relaxation of poses by molecular mechanics vmd 1.9.3 pymol 1.8.4 mgltools 1.5.6 amber18 gromacs2016.5 r3.5.1 plumed2.4 autodock4.2 openeye omega 2018.feb.1 openeye shape 2018.feb.1 openeye rocs 3.2.2.2 chemminer 3.32.1 fmcsr 1.22
m302c Thomas EvangelidisThomas evangelidis 20 2.31 2.55 0.95 homoligalign homoligalign