Grand Challenge 3 - Pose Prediction Method - Cathepsin S (Stage1B)

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
fojgi Oleg StroganovMolecular technologies, llc 24 1.3 2.13 2.13 leadfinder template docking leadfinder/buildmodel
dgsd5 Polo LamMax totrov 24 1.01 2.24 2.82 icm dock molsoft icm 3.8-5
g748e Alexandre BonvinAlexandre bonvin 24 1.93 2.67 1.63 haddock2.2 protein-ligand protocol haddock webserver 2.2 openeye omega 2017.6.1 openeye shape 2017.6.1 openeye rocs 3.2.2.2 chemminer 2.26 fmcsr 1.16
htav7 Bentley WingertCarlos camacho 24 1.92 2.83 2.38 dock_close smina feb 28 2016, based on autodock vina 1.1.2 openbabel 2.3.2 pymol 1.8.4.2 omega2 2.5.1.4 python 2.7.11 matplotlib 1.5.1 scipy 0.17.0 click 6.6
pj0v7 Dima KozakovDima kozakov 24 1.76 2.84 2.59 mc+md in-house monte-carlo, in-house minimization, rdkit, vina.
yetdj Ashutosh KumarKam zhang 24 2.7 3.12 1.89 popss omega 2.5.1 rocs 3.2.0 rosetta suite 2015.25
8byha Bogdan IorgaBogdan iorga 24 3.13 3.95 2.53 d3r-gc3-pose-best-rmsd-1b cactvs chemoinformatics toolkit v3.433/schrodinger suite 2016-1/corina v3.60/ucsf chimera v1.10.2/gold v5.2
tjtp6 Manon ReauMatthieu montes 24 3.83 4.3 2.36 rdock_hyde rdock 2013.1 / seesar 2016-12-08 / open babel 2.3.2
rr5gx Feng DingFeng ding 24 3.37 4.82 4.09 medusa-dock medusa-dock 1.1
qkoum Feng DingFeng ding 24 4.58 5.05 3.39 medusa-dock medusa-dock 1.1
i05zs Feng DingFeng ding 24 4.8 5.9 3.81 medusa-dock medusa-dock 1.1
ciam7 Manon ReauMatthieu montes 24 7.41 6.6 3.21 rdock_hyde_2 rdock 2013.1 / seesar 2016-12-08 / open babel 2.3.2
x3c8c Vikash KumarMolecular simulations and design group 24 6.56 7.09 2.64 structure-guided docking using glide open babel 2.3.2/ucsf chimera 1.11.2/maestro version 11.1.011
a7mwg Maria KadukovaGrudinin 24 8.45 7.74 3.04 convex-pl-mcmc-rrt-lowerclashes openbabel 2.3.2, rdkit 2017.03.3 for 3d coordinates generation; autodock vina and convex-pl for pose prediction, knodle for parametrization of small molecules
koq0o Anonymous AnonymousAnonymous 24 7.96 7.88 2.5 pl/mct-tess descriptors and libsvm based pose prediction method discovery studio 2017/omega 2.5/oedocking 3.0/entess/libsvm/matlab
qrqxk Maria KadukovaGrudinin 24 9.02 8.36 3.46 convex-pl-rrt openbabel 2.3.2, rdkit 2017.03.3 for 3d coordinates generation; autodock vina and convex-pl for pose prediction, knodle for parametrization of small molecules
khkgk Corentin/bryan/loic/dylan Bedart/dafniet/dreano/serillonM2 isdd students - paris-diderot university 24 8.22 8.37 2.19 m2isdd_protocol mgltools 1.5.6 / autodocktools 1.5.6 / autodock vina 1.1.2/ open babel 2.3.2 / open-source pymol 1.7.x / knime 3.4.0 + vsprep (gally, j. m., bourg, s., do, q.-t., aci-seche, s., bonnet, p., mol. inf., 36, 1700023 (2017))
8wv4r Bogdan IorgaBogdan iorga 24 8.31 8.49 4.67 d3r-gc3-pose-best-score-1b cactvs chemoinformatics toolkit v3.433/schrodinger suite 2016-1/corina v3.60/ucsf chimera v1.10.2/gold v5.2
rofmu Feng DingFeng ding 24 8.44 8.76 3.79 medusa-dock medusa-dock 1.1
x8o34 Maria KadukovaGrudinin 24 8.69 8.92 2.4 convex-pl-mcmc-rrt openbabel 2.3.2, rdkit 2017.03.3 for 3d coordinates generation; autodock vina and convex-pl for pose prediction, knodle for parametrization of small molecules
2ggkk Feng DingFeng ding 24 8.78 8.96 4.1 medusa-dock medusa-dock 1.1
r5tfm Manon RͩauMatthieu montes 24 7.64 9.36 7.46 rdock_vina_smina_hyde vina 1.1.2 (may11, 2011) / rdock 2013.1 / smina apr 2 2016. based on autodock vina 1.1.2. / seesar 2016-12-08 / open babel 2.3.2
nfvuj Jocelyn SunseriDavid koes 24 8.53 9.7 4.77 autodock vina docking with cnn scoring model rescoring docking performed with smina static binary available at https//sourceforge.net/projects/smina/files/ with default scoring function, then rescoring performed using gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina and the default cnn scoring model, conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py.
nwjvo Feng DingFeng ding 24 10.04 9.84 3.61 medusa-dock medusa-dock 1.1
oijuh Jocelyn SunseriDavid koes 24 7.33 10.05 8.51 autodock vina docking with cnn scoring model rescoring docking performed with smina static binary available at https//sourceforge.net/projects/smina/files/ with default scoring function, then rescoring performed using gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina and the default cnn scoring model, conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py.
g0of4 Jocelyn SunseriDavid koes 24 8.65 10.32 6.91 cnn docking with scoring model ranking docking performed with gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina , conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py.
fznsu Xiaoqin ZouXiaoqin zou 24 11.15 10.81 2.64 vina autodock vina 1.0
8siib Bing XieDavid d.l. minh 24 11.34 10.84 2.75 algdock openeye quacpac, modeller-9.18, ucsf dock6, ambertools 14, namd 2.9
x6ycn Jocelyn SunseriDavid koes 24 10.87 11.04 4.08 autodock vina baseline docking performed with smina static binary available at https//sourceforge.net/projects/smina/files/ with default scoring function, conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py.
kazpn Manon RͩauMatthieu montes 24 9.43 11.05 7.55 vina_hyde vina 1.1.2 (may11, 2011) / seesar 2016-12-08 / open babel 2.3.2
xe6c0 Jocelyn SunseriDavid koes 24 10.03 11.09 3.93 cnn docking with scoring model ranking docking performed with gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina , conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py.
gmedh Bing XieDavid d.l. minh 24 11.38 11.09 2.31 algdock openeye quacpac, modeller-9.18, ucsf dock6, ambertools 14, namd 2.9
0fsik Louis-philippe MorencyRafael j. najmanovich 24 10.83 11.14 3.97 flexaid openbabel v2.4 / flexaid / nrgsuite
ra8iu Xiaoqin ZouXiaoqin zou 24 10.62 11.19 4.6 a hierarchical docking method xdz_2 autodock vina 1.0/itscore2
bjws5 Bing XieDavid d.l. minh 24 11.35 11.31 2.95 algdock openeye quacpac, modeller-9.18, ucsf dock6, ambertools 14, namd 2.9
vtywu Jocelyn SunseriDavid koes 24 11.65 11.56 3.44 cnn docking with affinity model ranking docking performed with gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina, conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py.
raf3v Xiaoqin ZouXiaoqin zou 24 9.37 11.94 5.83 a hierarchical docking method xdz_2 autodock vina 1.0/itscore2
phfin Louis-philippe MorencyRafael j. najmanovich 24 10.96 11.95 4.4 flexaid___s openbabel v2.4 / flexaid___s / nrgsuite
ok5ko Anonymous AnonymousAnonymous 24 11.73 12.12 4.22 rhodium hts celpp 33678 method rhodium 380e9-x9/openbabel 2.3.90 / pymol 1.3
2bnbf Jonathan BohmannMedicinal and process chemistry 24 12.33 12.4 4.2 rhodium hts guided rhodium 380e9-x9/openbabel 2.3.90 / pymol 1.3
dbtcn Xiaoqin ZouXiaoqin zou 24 11.34 12.51 4.93 vina_wat autodock vina 1.0
7a76i Jocelyn SunseriDavid koes 24 16.2 12.57 8.48 autodock vina baseline docking performed with smina static binary available at https//sourceforge.net/projects/smina/files/ with default scoring function, conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py.
gi8u2 Anonymous AnonymousAnonymous 24 12.6 12.65 2.36 rhodium hts celpp 33678_2 method rhodium 380e9-x9/openbabel 2.3.90 / pymol 1.3
6wn6v Jocelyn SunseriDavid koes 24 12.41 12.88 3.51 autodock vina docking with cnn affinity model rescoring docking performed with smina static binary available at https//sourceforge.net/projects/smina/files/ with default scoring function, then rescoring performed using gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina and the default cnn affinity model, conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py.
7rokc Jocelyn SunseriDavid koes 24 17.66 15.71 6.21 cnn docking with affinity model ranking docking performed with gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina, conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py.
3prcf Manon RͩauMatthieu montes 24 18.6 16.04 7 smina_hyde smina apr 2 2016. based on autodock vina 1.1.2. / seesar 2016-12-08 / open babel 2.3.2
4pgvi Jocelyn SunseriDavid koes 24 19.33 16.23 5.94 autodock vina docking with cnn affinity model rescoring docking performed with smina static binary available at https//sourceforge.net/projects/smina/files/ with default scoring function, then rescoring performed using gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina and the default cnn affinity model, conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py.