hn0qy |
Zixuan Cang | Guo-wei wei |
19 |
-0.08 |
0.17 |
-0.1 |
0.23 |
tml-bp(consensus)/ri-score/gold/autodock-vina |
schrodinger, gold, autodock vina, r-tda, javaplex, scikit-learn |
structure-based scoring |
omotr |
Alexandre Bonvin | Alexandre bonvin |
19 |
-0.22 |
0.16 |
-0.25 |
0.23 |
haddock/prodigy scoring protocol |
haddock2.2 webserver / devel version of prodigy-lig |
structure-based scoring |
ru7zn |
Zhe Jia | Emil alexov, feng ding |
19 |
0.15 |
0.17 |
0.22 |
0.23 |
medusa 1.1 |
medusa 1.1 |
structure-based scoring |
4pakq |
Jocelyn Sunseri | David koes |
19 |
0.15 |
0.18 |
0.23 |
0.24 |
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. |
structure-based scoring |
vihk2 |
Xiaoqin Zou | Xiaoqin zou |
19 |
0.11 |
0.15 |
0.2 |
0.22 |
vina score |
vina score |
structure-based scoring |
3hz34 |
Minsup Kim | Cb2 / art e. cho |
19 |
0.31 |
0.17 |
0.4 |
0.23 |
qmmm/pbsa (quantum mechanics/molecular mechancis - poissonboltzmann surface area) |
qsite 6.6 |
structure-based scoring |
taqir |
Ashutosh Kumar | Kam zhang |
19 |
0.15 |
0.17 |
0.2 |
0.24 |
cdvs scoring |
maestro glide 6.1 |
structure-based scoring |
pgipt |
Jocelyn Sunseri | David koes |
19 |
0.4 |
0.16 |
0.6 |
0.21 |
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. |
structure-based scoring |
xz8so |
Oleg Stroganov | Molecular technologies, llc |
19 |
0.33 |
0.17 |
0.37 |
0.23 |
leadfinder baseline corrected minimum dg score |
leadfinder v 1708 |
structure-based scoring |
4jk3r |
Jocelyn Sunseri | David koes |
19 |
-0.04 |
0.17 |
-0.08 |
0.23 |
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. |
structure-based scoring |
vns3a |
Oleg Stroganov | Molecular technologies, llc |
19 |
0.07 |
0.17 |
0.13 |
0.23 |
leadfinder baseline dg score |
leadfinder v 1708 |
structure-based scoring |
zs7oa |
Zhe Jia | Emil alexov, feng ding |
19 |
0.23 |
0.16 |
0.37 |
0.22 |
delphi-gaussian dielectric mm/pbsa |
medusa 1.1/delphi 7.1/namd 2.11/amber 14/gaussian 09/vmd 1.9.3 |
structure-based scoring |
uwrw5 |
Zhe Jia | Emil alexov, feng ding |
19 |
0.23 |
0.16 |
0.37 |
0.22 |
delphi-gaussian dielectric mm/pbsa |
medusa 1.1/delphi 7.1/namd 2.11/amber 14/gaussian 09/vmd 1.9.3 |
structure-based scoring |
jg6d4 |
Bogdan Iorga | Bogdan iorga |
19 |
0.23 |
0.18 |
0.36 |
0.24 |
d3r-gc3-scoring-best-score-constraints |
cactvs chemoinformatics toolkit v3.433/schr̦dinger suite 2016-1/corina v3.60/ucsf chimera v1.10.2/gold v5.2 |
structure-based scoring |
hfbm5 |
Oleg Stroganov | Molecular technologies, llc |
19 |
0.28 |
0.17 |
0.35 |
0.23 |
leadfinder baseline corrected median dg score |
leadfinder v 1708 |
structure-based scoring |
m7oq4 |
Duc Nguyen | Guo-wei wei |
19 |
-0.05 |
0.17 |
-0.1 |
0.24 |
ri-score/tdl-bp/gold/autodock vina/schrodinger |
ri-score/tdl-bp/gold/autodock vina/schrodinger |
structure-based scoring |
5b5wz |
| |
19 |
0.21 |
0.17 |
0.28 |
0.23 |
openbabel/amber16/mgltools/autodock vina |
openbabel/amber16/mgltools/autodock vina method 1 |
structure-based scoring |
w83jw |
| |
19 |
0.18 |
0.18 |
0.25 |
0.24 |
glide docking |
glide in 2017-2 release |
structure-based scoring |
w6bwq |
Oleg Stroganov | Molecular technologies, llc |
19 |
0.22 |
0.16 |
0.3 |
0.22 |
leadfinder dg score on ensemble |
leadfinder v 1708 |
structure-based scoring |
xyy85 |
Duc Nguyen | Guo-wei wei |
19 |
-0.02 |
0.17 |
-0.06 |
0.23 |
ri-score/tdl-bp/gold/autodock vina/schrodinger |
ri-score/tdl-bp/gold/autodock vina/schrodinger |
structure-based scoring |
36ovr |
Sergei Grudinin | Grudinin |
19 |
0.18 |
0.16 |
0.27 |
0.23 |
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 |
structure-based scoring |
v3c55 |
Bogdan Iorga | Bogdan iorga |
19 |
0.1 |
0.18 |
0.16 |
0.25 |
d3r-gc3-scoring-best-rmsd |
cactvs chemoinformatics toolkit v3.433/schr̦dinger suite 2016-1/corina v3.60/ucsf chimera v1.10.2/gold v5.2 |
structure-based scoring |
etiak |
Xiaoqin Zou | Xiaoqin zou |
19 |
0.14 |
0.16 |
0.17 |
0.23 |
itscore2 |
itscore2 |
structure-based scoring |
vtuzm |
Polo Lam | Max totrov |
19 |
0.31 |
0.17 |
0.43 |
0.23 |
icm/apf 3d qsar |
molsoft icm 3.8-5 |
structure-based scoring |
3k3fn |
Dima Kozakov | Dima kozakov |
19 |
0.14 |
0.18 |
0.19 |
0.24 |
mc-refine |
in house monte-carlo/autodock vina/rdkit/ligsift |
structure-based scoring |
dhr26 |
Bogdan Iorga | Bogdan iorga |
19 |
0.22 |
0.17 |
0.26 |
0.23 |
d3r-gc3-scoring-best-score |
cactvs chemoinformatics toolkit v3.433/schr̦dinger suite 2016-1/corina v3.60/ucsf chimera v1.10.2/gold v5.2 |
structure-based scoring |
8uer8 |
Zhe Jia | Emil alexov, feng ding |
19 |
0.23 |
0.15 |
0.4 |
0.22 |
delphi-gaussian dielectric mm/pbsa |
medusa 1.1/delphi 7.1/namd 2.11/amber 14/gaussian 09/vmd 1.9.3 |
structure-based scoring |
oj2uj |
Zhe Jia | Emil alexov, feng ding |
19 |
0.28 |
0.16 |
0.41 |
0.22 |
delphi-gaussian dielectric mm/pbsa |
medusa 1.1/delphi 7.1/namd 2.11/amber 14/gaussian 09/vmd 1.9.3 |
structure-based scoring |
wcrem |
Bentley Wingert | Carlos camacho |
19 |
0.25 |
0.16 |
0.38 |
0.22 |
align_close |
smina feb 28 2016, based on autodock vina 1.1.2 openbabel 2.3.2 pymol 1.8.4.2 python 2.7.11 matplotlib 1.5.1 scipy 0.17.0 click 6.6 |
structure-based scoring |
q4sb0 |
Bentley Wingert | Carlos camacho |
19 |
0.25 |
0.16 |
0.39 |
0.22 |
dock_close |
smina feb 28 2016, based on autodock vina 1.1.2 openbabel 2.3.2 pymol 1.8.4.2 python 2.7.11 matplotlib 1.5.1 scipy 0.17.0 click 6.6 |
structure-based scoring |
fayra |
Jocelyn Sunseri | David koes |
19 |
0.05 |
0.17 |
0.06 |
0.24 |
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. |
structure-based scoring |
04kya |
Zixuan Cang | Guo-wei wei |
19 |
0.23 |
0.16 |
0.3 |
0.22 |
tml-bp/ri-score/gold/autodock-vina |
schrodinger, gold, autodock vina, r-tda, javaplex, scikit-learn |
structure-based scoring |
ppyff |
| |
19 |
0.15 |
0.17 |
0.18 |
0.23 |
maestro/mgltools/autodock vina |
maestro/mgltools/autodock vina method 1 |
structure-based scoring |
0qyrq |
Xiaoqin Zou | Xiaoqin zou |
19 |
0.03 |
0.17 |
0.11 |
0.24 |
vina score |
vina score |
structure-based scoring |
evkuh |
Jocelyn Sunseri | David koes |
19 |
0.37 |
0.16 |
0.55 |
0.22 |
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. |
structure-based scoring |
5r4cd |
Jonathan Bohmann | Medicinal and process chemistry |
19 |
-0.23 |
0.16 |
-0.37 |
0.22 |
rhodium hts / center-of-mass guided |
rhodium hts 380e9-x9 |
structure-based scoring |
uvjt0 |
Xiaoqin Zou | Xiaoqin zou |
19 |
0.03 |
0.17 |
0.03 |
0.24 |
itscore2 |
itscore2 |
structure-based scoring |
t3dbz |
Zixuan Cang | Guo-wei wei |
19 |
0.09 |
0.17 |
0.12 |
0.24 |
tdl-bp/ri-score/gold/autodock-vina |
schrodinger, gold, autodock vina, r-tda, javaplex, scikit-learn |
structure-based scoring |
72yx7 |
| |
19 |
-0.35 |
0.16 |
-0.5 |
0.22 |
pose filter ensemble (pfe) plus chemguass4 scoring method |
discovery studio 2017/omega 2.5/oedocking 3.0/pfe |
structure-based scoring |
tq8gb |
Duc Nguyen | Guo-wei wei |
19 |
0.04 |
0.17 |
0.05 |
0.24 |
ri-score/tdl-bp/gold/autodock vina/schrodinger |
ri-score/tdl-bp/gold/autodock vina/schrodinger |
structure-based scoring |
8vvhy |
Zhe Jia | Emil alexov, feng ding |
19 |
0.17 |
0.17 |
0.21 |
0.24 |
medusa 1.1 |
medusa 1.1 |
structure-based scoring |
f3ifz |
| |
19 |
0.16 |
0.17 |
0.22 |
0.23 |
openbabel/amber16/mgltools/autodock vina |
openbabel/amber16/mgltools/autodock vina method 1 |
structure-based scoring |
44mp4 |
Zixuan Cang | Guowei wei |
19 |
0.11 |
0.17 |
0.08 |
0.24 |
tml-bp/ri-score/gold/autodock-vina |
schrodinger, gold, autodock vina, r-tda, javaplex, scikit-learn |
structure-based scoring |
7ohx4 |
Alejandro Varela rial | Computational biophysics |
19 |
-0.21 |
0.17 |
-0.38 |
0.23 |
cnn deep affinity prediction |
mgltools-1.5.6/tensorflow1.2/autodock vina/rdkit2015.09.1 |
ligand-based scoring |
886g0 |
Thomas Evangelidis | Thomas evangelidis |
19 |
-0.05 |
0.17 |
-0.06 |
0.24 |
scaffopt_score6 |
ligprep v33013 scaffopt |
ligand-based scoring |
kevrd |
Alexandre Bonvin | Alexandre bonvin |
19 |
0.01 |
0.17 |
0.03 |
0.24 |
cathepsin-specific ligand-similarity based prediction |
chemminer, libsvm 3.21 |
ligand-based scoring |
drexw |
Thomas Evangelidis | Thomas evangelidis |
19 |
0.09 |
0.17 |
0.1 |
0.23 |
scaffopt_score8 |
ligprep v33013 scaffopt |
ligand-based scoring |
t6fkw |
Thomas Evangelidis | Thomas evangelidis |
19 |
0.2 |
0.17 |
0.29 |
0.24 |
scaffopt_score5 |
ligprep v33013 scaffopt |
ligand-based scoring |
dfagm |
Thomas Evangelidis | Thomas evangelidis |
19 |
0.09 |
0.17 |
0.1 |
0.23 |
scaffopt_score9 |
ligprep v33013 scaffopt |
ligand-based scoring |
kb2du |
Thomas Evangelidis | Thomas evangelidis |
19 |
0.08 |
0.17 |
0.16 |
0.23 |
scaffopt_score4 |
ligprep v33013 scaffopt |
ligand-based scoring |
2wz45 |
Thomas Evangelidis | Thomas evangelidis |
19 |
-0.11 |
0.17 |
-0.11 |
0.23 |
scaffopt_score7 |
ligprep v33013 scaffopt |
ligand-based scoring |
m5xb8 |
Thomas Evangelidis | Thomas evangelidis |
19 |
0.01 |
0.17 |
0.03 |
0.24 |
scaffopt_score3 |
ligprep v33013 scaffopt |
ligand-based scoring |
amspz |
Thomas Evangelidis | Thomas evangelidis |
19 |
0.08 |
0.17 |
0.14 |
0.24 |
scaffopt_score1 |
ligprep v33013 scaffopt |
ligand-based scoring |