Grand Challenge 3 - Pose Prediction Method - Cathepsin S (Stage1A)

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
yq6gg Ashutosh KumarKam zhang 24 2.05 2.39 0.95 omega/rocs/glide-refine omega 2.5.1 rocs 3.2.0 glide 6.1
djcq4 Ashutosh KumarKam zhang 24 2.6 2.6 0.95 popss omega 2.5.1 rocs 3.2.0 rosetta suite 2015.25
stjv8 Gregory WarrenNone 24 1.99 2.64 1.99 pcet posit v3.2.0.2
e7e0p Gregory WarrenNone 24 2.41 2.73 1.8 fpri posit v3.2.0.2; szybki v1.9.0.3; smzap 1.2.1.4
tr4ys Gregory WarrenNone 24 2.15 2.76 2.14 pdef posit v3.2.0.2
jodhp Bentley WingertCarlos camacho 24 1.96 2.78 2.24 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
b6t0o Polo LamMax totrov 24 1.7 2.82 2.76 icm dock molsoft icm 3.8-5
4ery5 Dima KozakovDima kozakov 24 2.23 2.97 2.31 mc-refine in house monte-carlo/ligsift/rdkit
sf5dj Alexandre BonvinAlexandre bonvin 24 2.23 3.04 2.03 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
ts6jd Bentley WingertCarlos camacho 24 2.53 3.14 2.25 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
e33k6 Bentley WingertCarlos camacho 24 2.53 3.14 2.25 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
rg5ed Ashutosh KumarKam zhang 24 2.31 3.14 1.94 cdvs omega 2.5.1 rocs 3.2.0 ligprep 2.8 glide 6.1
rm4m2 Anonymous AnonymousAnonymous 24 2.84 3.7 2.33 sybyl simularity suite, glide sybyl x-1.3, glide in schrodinger 2017-2 release
5addj Anonymous AnonymousAnonymous 24 3.21 3.78 2.87 gold/autodock vina/schrodinger/manual gold/autodock vina/schrodinger
csz33 Oleg StroganovMolecular technologies, llc 24 3.26 3.95 2.92 leadfinder template docking leadfinder/buildmodel
rk8tj Xiaoqin ZouXiaoqin zou 24 3.51 4.34 2.3 a template-based method, xdz_1 omega 2.5/shafts/amber11/itscore2
5pmnj Bogdan IorgaBogdan iorga 24 3.82 4.34 2.65 d3r-gc3-pose-best-score-constraints cactvs chemoinformatics toolkit v3.433/schrodinger suite 2016-1/corina v3.60/ucsf chimera v1.10.2/gold v5.2
tjwks Bogdan IorgaBogdan iorga 24 4.26 4.36 2.63 d3r-gc3-pose-best-rmsd cactvs chemoinformatics toolkit v3.433/schrodinger suite 2016-1/corina v3.60/ucsf chimera v1.10.2/gold v5.2
fcneq Vikash KumarMolecular simulations and design group 24 4.81 4.86 2.26 structure-guided docking using glide open babel 2.3.2/ucsf chimera 1.11.2/maestro version 11.1.011
gior3 Bogdan IorgaBogdan iorga 24 4.85 5.19 3.28 d3r-gc3-pose-best-score cactvs chemoinformatics toolkit v3.433/schrodinger suite 2016-1/corina v3.60/ucsf chimera v1.10.2/gold v5.2
fsi33 Anonymous AnonymousAnonymous 24 4.94 5.56 3.34 pl/mct-tess descriptors and libsvm based pose prediction method discovery studio 2017/omega 2.5/oedocking 3.0/entess/libsvm/matlab
ftbwp Sergei GrudininGrudinin 24 5.24 6.07 3.54 convex-pl 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
45h2u Corentin/bryan/loic/dylan Bedart/dafniet/dreano/serillonM2 isdd students - paris-diderot university 24 7.71 7.86 2.23 m2isdd_protocol mgltools 1.5.6 / autodocktools 1.5.6 / 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))
358c4 Anonymous AnonymousAnonymous 24 9.46 8.76 3.08 gold/autodock vina gold/autodock vina/schrodinger
8hvr2 Anonymous AnonymousAnonymous 24 10.21 9.46 2.85 gold/autodock vina/schrodinger gold/autodock vina/schrodinger
3cio8 Zhe JiaEmil alexov, feng ding 24 10.59 9.58 3.33 medusa-dock medusa-dock 1.1
ttb25 Xiaoqin ZouXiaoqin zou 24 10.63 9.89 2.82 a hierarchical docking method xdz_3 omega 2.5/shafts/mgltools/autodock vina 1.0
fmgze Xiaoqin ZouXiaoqin zou 24 8.26 9.92 5.02 a hierarchical docking method xdz_2 omega 2.5/shafts/mgltools/autodock vina 1.0/itscore2
trfpf Zhe JiaEmil alexov, feng ding 24 11.16 10.08 3.42 medusa-dock medusa-dock 1.1
shqkb Minsup KimCb2 / art e. cho 24 11.28 10.27 3.29 survival of the fittest algorithm (as implemented in qm-polarized ligand docking of schrodinger, ref cho, a. e.; guallar, v.; berne, b.; friesner, r. a., j. comput. chem., 2005, 26, 915-931) qm-polarized ligand docking (glide 6.6, qsite 6.6 and maestro 10.1 - schrodinger suites)
bgb8u Jocelyn SunseriDavid koes 24 10.21 10.69 3.31 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, ensemble of receptors chosen via pocketome.
fibez Anonymous AnonymousAnonymous 24 10.6 10.76 4.37 maestro/mgltools/autodock vina maestro/mgltools/autodock vina method 1
ugy74 Anonymous AnonymousAnonymous 24 11.02 10.8 3.63 openbabel/amber16/mgltools/autodock vina openbabel/amber16/mgltools/autodock vina method 1
p2har Anonymous AnonymousAnonymous 24 10.85 10.92 3.53 openbabel/amber16/mgltools/autodock vina method 1 openbabel/amber16/mgltools/autodock vina method 1
dpxzb Jocelyn SunseriDavid koes 24 9.64 11.22 3.76 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, ensemble of receptors chosen via pocketome.
ac4vz Jocelyn SunseriDavid koes 24 11.11 11.55 2.97 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, ensemble of receptors chosen via pocketome.
nnxyz Jocelyn SunseriDavid koes 24 11.69 12.25 2.64 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, ensemble of receptors chosen via pocketome.
zji7u Jonathan BohmannMedicinal and process chemistry 24 12.64 12.42 3.01 rhodium hts / center of mass guided rhodium 380e9-x9/openbabel 2.3.90 / pymol 1.3
sy6su Gregory WarrenNone 24 12.76 12.54 3.7 fhrs fred v3.2.0.2
jgwcj Gregory WarrenNone 24 12.85 12.62 3.46 fdef fred v3.2.0.2
0xj63 Jocelyn SunseriDavid koes 24 11.84 12.65 3.08 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, ensemble of receptors chosen via pocketome.
ppw0m Gregory WarrenNone 24 12.76 13.11 3.55 ccfs fred v3.2.0.2; smzap 1.2.1.4
un24c Gregory WarrenNone 24 13.32 13.25 3.53 pcfs fred v3.2.0.2; smzap 1.2.1.4
hdnka Alejandro Varela rialComputational biophysics 24 14.59 14.02 2.44 deep learning pharmacophore based docking htmd1.7.43/openbabel2.4.1/rdkit2015.09.1/cryptoscout/mgltools-1.5.6/acemd3/