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. Author manuscript; available in PMC: 2021 Feb 1.
Published in final edited form as: J Comput Aided Mol Des. 2020 Jan 23;34(2):99–119. doi: 10.1007/s10822-020-00289-y

Table 4.

Top 10 submissions, based on RMSEc, for each free energy prediction challenge. See Table 3 for details.

RMSEc Software Submitter/PI Organization Submission ID
BACE1 Stage 1
1.39 deepscaffopt T. Evangelidis/T. Evangelidis Uochb & Ceitec xhxwo
1.41 itscore X. Xu/X. Zou University of Missouri-Columbia ri7k3
1.42 deepscaffopt T. Evangelidis/T. Evangelidis Uochb & Ceitec fmju8
1.47 rdkit / mgltools/ smina (modified) R. Quiroga/M. Villarreal Universidad Nacional De Cordoba Argentina m20gt
1.47 htmd1.13.8/acemd3/rdkit2018.03.4/mmenergy/deltadelta protein forcefield amber ligand forcefield amber water model tip3 A. Varela Rial/G. De Fabritiis Acellera gcjgs
1.55 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
1.73 gromacs, g_mmpbsa, acpype protein forcefield amber ligand forcefield gaff amber14 water model tip3p A. Stander/A. Stander University of Pretoria cphi3
1.73 schrodinger (2018–2) protein forcefield opls_2005 ligand forcefield opls_2005 water model no water model is used in this method P. Chen/Department of High Performance Computing Application, National Supercomputer Center in Guangzhou (NSCC-GZ) Sun Yet-Sen University efemt
2.14 tensorflow X. Xu/X. Zou University of Missouri-Columbia wmkp3
4.7 autodock vina 1.1.2/rdkit 2018.03.1/openbabel/pymol/fkcombu/acpype/gromacs 5.1.5/g_mmpbsa protein forcefield amber99sb-ildn ligand forcefield gaff water model tip3p T. wang None yuxiz
BACE1 Stage 2
1.22 htmd1.13.8/rdkit2018.03.4/kdeep A. Varela Rial/G. De Fabritiis Acellera 5mxnz
1.24 ag/dg/tdl-bp/schrodinger K. Gao;D. Nguyen/W. Guo-Wei Michigan State University, East Lansing, Mi 8frur
1.27 rdkit/gnina/smina P. Francoeur/D. Koes University of Pittsburgh u2v0p
1.29 ag/dg/tdl-bp/schrodinger M. Wang;D. Nguyen/W. Guo-Wei Michigan State University, East Lansing, Mi ae6kd
1.3 rdkit/gnina/smina P. Francoeur/D. Koes University of Pittsburgh gdczi
1.33 deepscaffopt T. Evangelidis/T. Evangelidis Uochb & Ceitec 0drpa
1.33 deepscaffopt T. Evangelidis/T. Evangelidis Uochb & Ceitec 87eyt
1.34 ag/dg/tdl-bp/schrodinger M. Wang;D. Nguyen/W. Guo-Wei Michigan State University, East Lansing, Mi bxuha
1.35 ag/dg/tdl-bp/schrodinger D. Nguyen/W. Guo-Wei Michigan State University, East Lansing, Mi 0oaoj
1.36 rdkit/gnina/smina P. Francoeur/D. Koes University of Pittsburgh yz8ty
CatS
0.47 ag/dg/tdl-bp/schrodinger K. Gao;D. Nguyen/W. Guo-Wei Michigan State University, East Lansing, Mi ar5p6
0.48 ag/dg/tdl-bp/schrodinger D. Nguyen/W. Guo-Wei Michigan State University, East Lansing, Mi 24b03
0.49 maestro/schrodinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p J. Zou/C. Simmerling Stony Brook University 3gjm2
0.49 maestro/schrodinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p J. Zou/C. Simmerling Stony Brook University tkkqh
0.5 maestro/schrodinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p J. Zou/C. Simmerling Stony Brook University 53cvi
0.5 maestro/schrodinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p J. Zou/C. Simmerling Stony Brook University szgth
0.5 ag/dg/tdl-bp/schrodinger K. Gao;D. Nguyen/W. Guo-Wei Michigan State University, East Lansing, Mi qian4
0.53 deepscaffopt T. Evangelidis/T. Evangelidis Uochb & Ceitec ffnbb
0.53 deepscaffopt T. Evangelidis/T. Evangelidis Uochb & Ceitec i7kce
0.54 deepscaffopt T. Evangelidis/T. Evangelidis Uochb & Ceitec k4gpy