Table 3.
Top 10 submissions, based on Kendall’s τ, for each free energy prediction challenge. See Table 3 for details.
| Kendall’s τ | Software | Submitter/PI | Organization | Submission ID |
|---|---|---|---|---|
| BACE1 Stage 1 | ||||
| 0.42 | amber16, ambertools17, as-ie (developed by our own laboratory, doi10.1021/acs.jctc.7b01295) protein forcefield ff14sb ligand forcefield gaff water model tip3p | J. Bao/J. Zhang | East China Normal University | t4eb6 |
| 0.31 | rdkit / mgltools/ smina (modified) | R. Quiroga/M. Villarreal | Universidad Nacional De Cordoba Argentina | m20gt |
| 0.28 | gromacs, g_mmpbsa, acpype protein forcefield amber ligand forcefield gaff amber14 water model tip3p | A. Stander/A. Stander | University of Pretoria | cphi3 |
| 0.25 | homoligalign, sqm/cosmo protein forcefield amber14sb ligand forcefield gaff2 water model tip3p | T. evangelidis/P. Hobza | Uochb & Ceitec | 7x3ay |
| 0.24 | homoligalign, sqm/cosmo protein forcefield amber14sb ligand forcefield gaff2 water model tip3p | T. evangelidis/P. Hobza | Uochb & Ceitec | nos76 |
| 0.24 | omega 3/datawarrior 4.7.3/smina version apr. 29, 2017 with vinardo scoring function/rf-score vs v2 | B. Wang/H. NG | Kansas State University | ugrpw |
| 0.21 | itscore | X. Xu/X. Zou | University of Missouri-Columbia | ri7k3 |
| 0.17 | amber18 for md, amber16 for mmpbsa.py protein forcefield amberff19sb ligand forcefield gaff2 water model tip3p | S. Sasmal; L. El Khoury/D. Mobley | University of California, Irvine | 7f74g |
| 0.16 | deepscaffopt | T. Evangelidis/T. Evangelidis | Uochb & Ceitec | xhxwo |
| 0.14 | deepscaffopt | T. Evangelidis/T. Evangelidis | Uochb & Ceitec | fmju8 |
| BACE1 Stage 2 | ||||
| 0.59 | htmd1.13.8/rdkit2018.03.4/kdeep | A. Varela Rial/G. De Fabritiis | Acellera | 5mxnz |
| 0.42 | ag/dg/tdl-bp/schrodinger | K. Gao;D. Nguyen/W. Guo-Wei | Michigan State University, East Lansing, Mi | 8frur |
| 0.36 | rdkit/gnina/smina | P. Francoeur/D. Koes | University of Pittsburgh | gdczi |
| 0.31 | rdkit/gnina/smina | P. Francoeur/D. Koes | University of Pittsburgh | u2v0p |
| 0.3 | ag/dg/tdl-bp/schrodinger | M. Wang;D. Nguyen/W. Guo-Wei | Michigan State University, East Lansing, Mi | ae6kd |
| 0.29 | deepscaffopt | T. Evangelidis/T. Evangelidis | Uochb & Ceitec | 0drpa |
| 0.28 | deepscaffopt | T. Evangelidis/T. Evangelidis | Uochb & Ceitec | 87eyt |
| 0.26 | ag/dg/tdl-bp/schrodinger | D. Nguyen/W. Guo-Wei | Michigan State University, East Lansing, Mi | 0oaoj |
| 0.25 | ag/dg/tdl-bp/schrodinger | M. Wang;D. Nguyen/W. Guo-Wei | Michigan State University, East Lansing, Mi | bxuha |
| 0.22 | rdkit/gnina/smina | P. Francoeur/D. Koes | University of Pittsburgh | yz8ty |
| CatS | ||||
| 0.62 | maestro/schrodinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p | J. Zou/C. Simmerling | Stony Brook University | |
| 0.62 | maestro/schrodinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p | T. Chuan/C. Simmerling | Stony Brook University | 3gjm2 |
| 0.61 | maestro/schrodinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p | J. Zou/C. Simmerling | Stony Brook University | tkkqh |
| 0.61 | maestro/schrodinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p | T. Chuan/C. Simmerling | Stony Brook University | 53cvi |
| 0.48 | ag/dg/tdl-bp/schrodinger | D. Nguyen/W. Guo-Wei | Michigan State University, East Lansing, Mi | szgth |
| 0.47 | ag/dg/tdl-bp/schrodinger | K. Gao;D. Nguyen/W. Guo-Wei | Michigan State University, East Lansing, Mi | 24b03 |
| 0.45 | ag/dg/tdl-bp/schrodinger | K. Gao;D. Nguyen/W. Guo-Wei | Michigan State University, East Lansing, Mi | qian4 |
| 0.34 | ag/dg/tdl-bp/schrodinger | M. Wang;D. Nguyen/W. Guo-Wei | Michigan State University, East Lansing, Mi | ar5p6 |
| 0.33 | deepscaffopt | T. Evangelidis/T. Evangelidis | Uochb & Ceitec | jxb8i |
| 0.3 | deepscaffopt | T. Evangelidis/T. Evangelidis | Uochb & Ceitec | ffnbb |