| 0cdix |
Antonia Mey | Julien michel |
20 |
8.09 |
6.99 |
4.8 |
flare_docking |
flare 2.0.0 revision 34140 |
| 0fgte |
Rodrigo Quiroga | Villarreal marcos |
20 |
2.96 |
5.31 |
4.28 |
2vinardo-beta |
rdkit / mgltools/ smina (modified) |
| 0invp |
Kaifu Gao | Guowei wei |
20 |
0.56 |
0.81 |
0.57 |
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 Iorga | Bogdan iorga |
20 |
0.83 |
1.46 |
2.07 |
d3r-gc4-pose-bestscore-phase-1a |
cactvs chemoinformatics toolkit v3.433/schr̦dinger suite 2018-1/corina v3.60/ucsf chimera v1.10.2/gold v5.2 |
| 37v4p |
Bentley Wingert | Carlos camacho |
20 |
1.25 |
1.47 |
0.91 |
dock close |
openbabel 2.3.2 maestro 2018-3 prime smina apr 2 2016 |
| 3i0ua |
Manon RÌ©au | Matthieu montes |
20 |
1.74 |
1.96 |
1.03 |
rdock_adt |
icon/chemaxon/rdock/autodock 4.2 |
| 4h67m |
Paul Francoeur | David koes |
20 |
4.6 |
5.43 |
2.71 |
aligned autodock vina |
rdkit/gnina/smina |
| 4x5a8 |
Dima Kozakov | Dima kozakov |
20 |
0.64 |
0.77 |
0.34 |
macrocycle align |
brikard, libmol , rdkit, openbabel, |
| 54duu |
Cyril, naÌøm, edouard Bigot, husain, mahieu | University paris diderot |
20 |
2.11 |
5.45 |
4.66 |
knime/rdkit/chemaxon/mgltools/autodock vina |
knime/rdkit/chemaxon/mgltools/autodock vina |
| 5iz88 |
Paul Francoeur | David koes |
20 |
45.06 |
44.08 |
5.01 |
blind cnn |
rdkit/gnina/smina |
| 5t302 |
Kaifu Gao | Guowei wei |
20 |
0.55 |
0.81 |
0.58 |
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 Forli | Forli |
20 |
1.31 |
1.29 |
0.32 |
autodock 4.x gpu with visual inspection |
autodock 4.x gpu |
| 7yni2 |
Manon RÌ©au | Matthieu montes |
20 |
2.41 |
3.24 |
2.33 |
rdock_seesar |
icon/chemaxon/rdock/seesar |
| apue7 |
Attilio Vargiu | Attilio vittorio vargiu |
20 |
3.17 |
4.75 |
3.42 |
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 khoury | David mobley |
20 |
1.34 |
1.56 |
0.86 |
omega/hybrid/mm-gbsa |
omega 3.0.8/hybrid 3.2.0.2/mm-gbsa/amber16 |
| biw3a |
Maria Kadukova | Sergei grudinin |
20 |
1.64 |
1.82 |
0.97 |
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 Kadukova | Sergei grudinin |
20 |
2.36 |
2.64 |
1.87 |
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 Kadukova | Sergei grudinin |
20 |
3.39 |
3.99 |
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 Francoeur | David koes |
20 |
46.52 |
46.36 |
0.98 |
blind autodock vina |
rdkit/gnina/smina |
| dg3gy |
Alexandre Bonvin | Alexandre bonvin |
20 |
1.94 |
1.97 |
0.89 |
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 Kumar | Kam zhang |
20 |
1.07 |
1.29 |
0.69 |
popss-lite |
omega 3.0.0.1 rocs 3.2.2.2 glide 6.1 |
| e2pw6 |
Par Soderhjelm | Soderhjelm research group |
20 |
5 |
5.49 |
3.42 |
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 Wang | Ho-leung ng |
20 |
2.6 |
13.26 |
20.2 |
semi-crossdocking with vinardo |
autodock-vina/smina-vinardo/fragfp-datawarrior/openbabel 2.4.1/openeye-omega |
| epvj2 |
Manon RÌ©au | Matthieu montes |
20 |
2.45 |
3.17 |
2.97 |
vina_rdock |
icon/chemaxon/mgltools/autodock vina/rdock |
| f4rwu |
Woong-hee Shin | Daisuke kihara |
20 |
8 |
7.46 |
3.08 |
docking pose rescoring using pl-patchsurfer |
autodock vina 1.1.2 pl-patchsurfer2 |
| fky0k |
Polo Lam | Max totrov |
20 |
0.74 |
0.93 |
0.45 |
icm dock with 4d receptor ensemble and apf ligand bias |
molsoft icm 3.8-7b |
| gd5eo |
Manon RÌ©au | Matthieu montes |
20 |
1.74 |
2.03 |
1.16 |
rdock_vina |
icon/chemaxon/rdock/vina |
| gduxh |
Manon RÌ©au | Matthieu montes |
20 |
2.27 |
2.38 |
1.5 |
vina_rdock_solv |
icon/chemaxon/mgltools/autodock vina/rdock_solv |
| gynvw |
Manon RÌ©au | Matthieu montes |
20 |
1.78 |
2.2 |
1.64 |
vina_vina |
icon/chemaxon/mgltools/autodock vina |
| i065y |
Sukanya/lea Sasmal/el khoury | David mobley |
20 |
1.88 |
1.87 |
0.69 |
omega/hybrid/mm-gbsa |
omega 3.0.8/hybrid 3.2.0.2/mm-gbsa/amber16 |
| i82td |
Oleg Stroganov | Biomoltech inc. |
20 |
1.42 |
1.52 |
0.64 |
lead finder + xedex conformer sampling |
lead finder 1808, xedex, build model 1808 |
| isy26 |
Manon RÌ©au | Matthieu montes |
20 |
1.84 |
1.84 |
0.66 |
rdock_rdock |
icon/chemaxon/rdock |
| ix3cv |
Paul Francoeur | David koes |
20 |
4.6 |
5.24 |
2.6 |
aligned cnn |
rdkit/gnina/smina |
| jit54 |
Maria Kadukova | Sergei grudinin |
20 |
2.36 |
2.64 |
1.87 |
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 Yang | Yingkai zhang |
20 |
1.09 |
1.55 |
1.59 |
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 Yang | Submitter Last Name: Yang Submitter First Name: Chao Submitter Email: cy1063@nyu.edu Submitter Organization: New York University |
20 |
1.06 |
1.15 |
0.33 |
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 Vargiu | Attilio vittorio vargiu |
20 |
3.09 |
4.1 |
2.7 |
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 Zou | Ho-leung ng |
20 |
15.52 |
22.38 |
21.88 |
semi-crossdocking with vinardo and energy minimization. |
autodock-vina/smina-vinardo/fragfp-datawarrior/openbabel 2.4.1/openeye-omega/yasara |
| m0yfh |
Cyril, naÌøm, edouard Bigot, husain, mahieu | University paris diderot |
20 |
8 |
6.62 |
2.65 |
knime/rdkit/chemaxon/mgltools/autodock vina |
knime/rdkit/chemaxon/mgltools/autodock vina |
| m7t0w |
Andre Stander | Dr andre stander |
20 |
1.25 |
1.45 |
0.73 |
grambina |
grambina, amber, gromacs, chimera, rdkit |
| maej5 |
Maria Kadukova | Sergei grudinin |
20 |
3.39 |
3.99 |
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 |
| nstab |
Attilio Vargiu | Attilio vittorio vargiu |
20 |
1.81 |
3.14 |
2.93 |
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 |
| nwm5a |
Alexandre Bonvin | Alexandre bonvin |
20 |
1.4 |
1.66 |
0.84 |
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 RÌ©au | Matthieu montes |
20 |
1.71 |
1.69 |
0.7 |
champion's_list |
icon/chemaxon/rdock/vina/seesar/autodock 4.2/rdock_solv |
| oen8j |
Manon RÌ©au | Matthieu montes |
20 |
1.91 |
1.93 |
0.69 |
rdock_rdock_solv |
icon/chemaxon/rdock/rdock_solv |
| ooptr |
Ashutosh Kumar | Kam zhang |
20 |
1.13 |
1.31 |
0.61 |
popss |
omega 3.0.0.1 rocs 3.2.2.2 rosetta suite 2015.25 |
| pbt5s |
Cheng Peng | Weiliang zhu |
20 |
3.26 |
3.75 |
2.54 |
2d-remd |
maestro gromacs 5.1.4 plumed 2.3.3 |
| pe6zg |
Attilio Vargiu | Attilio vittorio vargiu |
20 |
2.22 |
3.05 |
2.51 |
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 Chen | Chen Pin |
20 |
6.57 |
7.04 |
2.7 |
pin chen |
schrodinger (glide tools) (2018-2 version) for docking,sitemap tools for binding sites predicting. |
| qjto3 |
Bentley Wingert | Carlos camacho |
20 |
1.23 |
1.37 |
0.93 |
dock close manual |
openbabel 2.3.2 maestro 2018-3 prime smina apr 2 2016 |
| qk28f |
Hasan h. Ince | Hasan h. ince |
20 |
8.9 |
14.23 |
9.49 |
drugitt docking protocol |
in-house |
| qqou3 |
Alejandro Varela rial | Gianni de fabritiis |
20 |
1.02 |
1.33 |
0.71 |
skeledock |
htmd1.13.8/acemd2/rdkit2018.03.4 |
| qz5tn |
Manon RÌ©au | Matthieu montes |
20 |
1.78 |
2.2 |
1.64 |
vina_adt |
icon/chemaxon/mgltools/autodock vina/autodock 4.2 |
| rapwf |
Bogdan Iorga | Bogdan iorga |
20 |
0.83 |
1.1 |
0.63 |
d3r-gc4-pose-bestpose-phase-1a |
cactvs chemoinformatics toolkit v3.433/schr̦dinger suite 2018-1/corina v3.60/ucsf chimera v1.10.2/gold v5.2 |
| rwov6 |
| |
20 |
3.67 |
3.61 |
1.53 |
molecular similarity/ ligand alignment |
rdkit (2018.03.4) / moe (2018.0101) / swiss-model |
| s4fu0 |
Maria Kadukova | Sergei grudinin |
20 |
4.62 |
5.47 |
3.35 |
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 Soderhjelm | Soderhjelm research group |
20 |
2.96 |
4.34 |
2.83 |
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 Forli | Forli |
20 |
1.45 |
1.55 |
0.68 |
autodock 4.x gpu with substructure filters |
autodock4.x gpu/openbabel/python |
| skftb |
Manon RÌ©au | Matthieu montes |
20 |
11.71 |
11.12 |
2.59 |
vina_seesar |
icon/chemaxon/mgltools/autodock vina/seesar |
| t3ddc |
Xianjin Xu | Xiaoqin zou |
20 |
1.02 |
1.06 |
0.57 |
a hierarchical docking method xdz_1 |
maestro/openeye/mgltools/autodock vina |
| tm8kw |
Stefano Forli | Forli |
20 |
1.92 |
2.35 |
1.53 |
autodock 4.x gpu |
autodock4.x gpu/openbabel/python |
| uf8ik |
Jamal Shamsara | Jamal shamsara |
20 |
10.22 |
9.34 |
2.32 |
pose prediction using flexx |
leadit 2.3.2/chem 3d 2016# |
| uq8b0 |
| |
20 |
0.72 |
0.94 |
0.65 |
similarity/alignment/minimization |
rdkit/torch/macromodel |
| uqapi |
Benjamin Brown | Jens meiler |
20 |
5.98 |
5.77 |
3.14 |
bclmolalign |
bcl v3.5, corina v4.1.0 |
| wp8n0 |
| |
20 |
2.31 |
2.42 |
0.68 |
ligand_shape_similarity_flexible_alignment |
autodock vina 1.1.2/rdkit 2018.03.1/openbabel/pymol/fkcombu |
| xdd3r |
Hahnbeom Park | Institute for protein design |
20 |
0.96 |
1.2 |
0.8 |
rosetta gadock |
rosetta (pre-release version, git hash 845e653c80ec0965c63afa747b6c7efde2ef63b8)/corina classic, webserver version/openbabel-2.4.1/antechamber-17.3 |
| xgctb |
Benjamin Brown | Jens meiler |
20 |
5.47 |
5.63 |
3.28 |
bclmolalign with protein-ligand complex energy minimization |
bcl v3.5, corina v4.1.0, moe 2018.01 |
| xpien |
Jonathan Bohmann | Medicinal and process chemistry |
20 |
3.88 |
4.33 |
1.62 |
ligandmatch |
ligandmatch 1.0 openbabel 2.3.90 |
| xsm5f |
Alexandre Bonvin | Alexandre bonvin |
20 |
3.37 |
4.95 |
3.76 |
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 |
2.61 |
2.78 |
1.33 |
ligand_shape_similarity_vina_docking |
autodock vina 1.1.2/rdkit 2018.03.1/openbabel/pymol/fkcombu/acpype/gromacs 5.1.5 |
| yw3a0 |
Carlos Modenutti | Marcelo marti |
20 |
1.02 |
1.3 |
1.19 |
dockq |
moe2016.08/autodock4/mgltools1.5.7rc1/amber16/ligprep/rdkit2018-3 |
| zav0x |
Ashutosh Kumar | Kam zhang |
20 |
1.13 |
1.2 |
0.54 |
popss-pb |
omega 3.0.0.1 rocs 3.2.2.2 szybki 1.9.0.3 |
| zb4ps |
Cyril, naÌøm, edouard Bigot, husain, mahieu | University paris diderot |
20 |
4.83 |
4.75 |
1.71 |
knime/rdkit/chemaxon/mgltools/autodock vina |
knime/rdkit/chemaxon/mgltools/autodock vina |
| m302c |
Thomas Evangelidis | Thomas evangelidis |
20 |
2.43 |
2.67 |
1.06 |
homoligalign |
homoligalign |