Table 5.
Top 3 submissions, based on Kendall’s τ, for each affinity ranking challenge. Submission ID in bold font indicates a method that used machine learning. See Table 3 for details.
| Kendall’s Tau | Software | Submitter/PI | Organization | Submission ID |
|---|---|---|---|---|
| Cats Stage 1 | ||||
| 0.45 | molsoft icm 3.8–5 | P. Lam/M.Totrov | Molsoft | vtuzm |
| 0.36 | chemminer, libsvm 3.21 | A. Bonvin/A. Bonvin | Utrecht University | kevrd |
| 0.35 | ligprep v33013 scaffopt | T. Evangelidis/T. Evangelidis | Central European Institute of Technology | kb2du |
| Cats Stage 2 | ||||
| 0.39 | molsoft icm 3.8–7 | P. Lam/M.Totrov | Molsoft | q2k8y |
| 0.34 | ligprep v33013 scaffopt | T. Evangelidis/T. Evangelidis | Central European Institute of Technology | m6yb2 |
| 0.32 | ligprep v33013 scaffopt | T. Evangelidis/T. Evangelidis | Central European Institute of Technology | e4emg |
| ABL1 | ||||
| 0.52 | rhodium 380e9–x9/openbabel 2.3.90 / pymol 1.3 | J. Bohmann/Medicinal and Process Chemistry | Southwest Research Institute | 3o8xi |
| 0.52 | schrodinger, gold, autodock vina, r-tda, javaplex, sci kit-learn | Z. Cang/W. Guo-Wei | Michigan State University | rdn3k |
| 0.43 | ri-score/tdl-bp/autodock vina | D. Nguyen/W. Guo-Wei | Michigan State University | c4xt7 |
| JAK2 SC2 | ||||
| 0.55 | 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. | J. Sunseri/D. Koes | University of Pittsburgh | zdyb5 |
| 0.36 | molsoft icm 3.8–6 | P. Lam/M.Totrov | Molsoft | 7yjh3 |
| 0.23 | amber11 | X.Zou/X. Zou | University of Missouri-Columbia | qnq6x |
| JAK2 SC3 | ||||
| 0.71 | itscore2 | X. Zou/X. Zou | University of Missouri-Columbia | 87mci |
| 0.6 | docking performed with gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina, conformer generation performed with rdkit viahttps//github.com/dkoes/rdkit-scripts/rdconf.py, ensemble of receptors chosen via pocketome. | J. Sunseri/D. Koes | University of Pittsburgh | 7bi2k |
| 0.56 | 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. | J. Sunseri/D. Koes | University of Pittsburgh | yghq5 |
| p38-α | ||||
| 0.21 | molsoft icm 3.8–6 | P. Lam/M. Totrov | Molsoft | 8b6kk |
| 0.2 | 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 | B. Wingert/C. Camacho | University of Pittsburgh | u48q2 |
| 0.13 | 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 | B. Wingert/C. Camacho | University of Pittsburgh | 5vy6c |
| TIE2 | ||||
| 0.57 | ri-score/tdl-bp/autodock vina | D. Nguyen/W. Guo-Wei | Michigan State University | uuihe |
| 0.57 | schrodinger, gold, autodock vina, r-tda, javaplex, scikit-learn | Z. Cang/W. Guo-Wei | Michigan State University | y7qxv |
| 0.5 | 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. | J. Sunseri/D. Koes | University of Pittsburgh | xpmn7 |
| VEGFR2 | ||||
| 0.43 | molsoft icm 3.8–6 | P. Lam/M. Totrov | Molsoft | y0048 |
| 0.4 | itscore2 | X.Zou/X. Zou | University of Missouri-Columbia | uv5tc |
| 0.38 | chemminer, libsvm 3.21 | A. Bonvin/A. Bonvin | Utrecht University | 7smbe |