GC3 Active/Inactive Classification - Cathepsin S (Stage 2)

Grand Challenge 3 - Active/Inactive Classification - Cathepsin S (Stage 2)

Kendall's τ

RMSEc

Pearson's r

Spearman's ρ

Receipt ID Submitter Name PI/Group Name Number of Ligands Kendall's τ Kendall's τ Error Spearman's ρ Spearman's ρ Error Pearson's r Pearson's r Error RMSEc RMSEc Error Method Name Software Method Type
js3r3 Bogdan IorgaBogdan iorga 33 0.25 0.12 0.35 0.17 0.43 0.15 2.81 0.35 alchemical free energy calculation Name: Alchemical Free Energy Calculation Software: Gromacs, PMX Protein Forcefield: OPLS-AA forcefield Ligand Forcefield: OPLS-AA forcefield Water Model: TIP4P Parameter: Assumed pH 7.0 Parameter: 10 ns Molecular Dynamics simulations at 300 K. Integrator : sd. Berendsen pressure coupling. Parameter: Morphing : Short 50 ps MD at 300 K on 200 extracted conformations from state A and state B simulations. Parameter: Morphing : sc-alpha = 0.5, sc-sigma = 0.25. Parameter: Morphing : Integrator : md. Pressure coupling : berendsen. Temperature coupling : velocity rescale Method: The protein used for free energy calculation was taken from the structure QJAN. Ligands 3D coordinates were obtained by docking using Glide and SP protocol, with constraints applied on the common substructure with either CatS_15, CatS_20 or CatS_24. Alchemical free energies were calculated using Gromacs and OPLS-AA force field, some scripts from the PMX software and some in house developed scripts. Hybrid structures and topologies were built using a modified version of the MOL2FF package developed in our team. CatS_67 was used as reference structure for the free energy calculations. Equilibrium 10 ns MD simulations were performed for the two states (corresponding to lambda 0 and 1), using Gromacs and OPLS-AA force field. Snapshots from the equilibrium runs were extracted to spawn 100 simulations of 50 ps each to alchemically morph between the two states of the system. The work values over every non-equilibrium transition were extracted and further used to estimate the free energy differences relying on the Crooks Fluctuation Theorem and utilizing Crooks-Gaussian Intersection as estimator. Answer 1: Yes free energy
wdgzp    33 0.21 0.12 0.29 0.17 0.24 0.14 1.01 0.14 amber/mmpbsa/elie amber protein forcefield ff14sb ligand forcefield gaff (resp charges, at hf6-31g* level) water model tip3 structure-based score
6xwau    33 0.21 0.12 0.28 0.17 0.24 0.15 1.02 0.14 amber/mmpbsa/elie amber protein forcefield ff14sb ligand forcefield gaff (resp charges, at hf6-31g* level) water model tip3 structure-based score
y74up    33 0.08 0.13 0.13 0.19 0.06 0.19 1.27 0.19 amber/mmpbsa/elie amber protein forcefield ff14sb ligand forcefield gaff (resp charges, at hf6-31g* level) water model tip3 structure-based score
ioe5x    33 0.12 0.13 0.18 0.19 0.19 0.19 1.32 0.19 amber/mmpbsa/elie amber protein forcefield ff14sb ligand forcefield gaff (resp charges, at hf6-31g* level) water model tip3 structure-based score
bxxm2    33 0.01 0.13 0.03 0.19 0.02 0.19 1.52 0.21 amber/mmpbsa/elie amber protein forcefield ff14sb ligand forcefield gaff (resp charges, at hf6-31g* level) water model tip3 structure-based score
6grpy Xiaoqin ZouXiaoqin zou 33 0.04 0.12 0.03 0.18 -0.05 0.17 2.9 0.36 mmpbsa amber11 protein forcefield amber03 force field ligand forcefield generalized amber force field (gaff) (am1-bcc charges) water model tip3p structure-based score
grhvk Bentley WingertCarlos camacho 33 0.27 0.11 0.41 0.16 0.48 0.13 0.73 0.11 quasi-exact smina feb 28 2016, based on autodock vina 1.1.2 openbabel 2.3.2 pymol 1.8.4.2 omega2 2.5.1.4 python 2.7.11 matplotlib 1.5.1 scipy 0.17.0 click 6.6 protein forcefield smina docking ligand forcefield smina docking water model smina docking parameter default structure-based score
hnzvf Bentley WingertCarlos camacho 33 -0.27 0.11 -0.41 0.15 -0.48 0.13 1.17 0.14 quasi-exact smina feb 28 2016, based on autodock vina 1.1.2 openbabel 2.3.2 pymol 1.8.4.2 omega2 2.5.1.4 python 2.7.11 matplotlib 1.5.1 scipy 0.17.0 click 6.6 protein forcefield smina docking ligand forcefield smina docking water model smina docking parameter default structure-based score
v4jv4 Duc NguyenGuo-wei wei 33 -0.05 0.12 -0.07 0.18 -0.15 0.18 1.06 0.15 ri-score-k1-v/tdl-bp/autodock vina ri-score,tdl-bp,autodock vina,schrodinger protein forcefield opls3 ligand forcefield opls3 water model spc structure-based score
pb0ck Duc NguyenGuo-wei wei 33 -0.07 0.13 -0.1 0.18 -0.06 0.18 0.98 0.14 ri-score-k1-v/tdl-bp/autodock vina ri-score,tdl-bp,autodock vina,schrodinger protein forcefield opls3 ligand forcefield opls3 water model spc structure-based score
qt5di Duc NguyenGuo-wei wei 33 0.03 0.13 0 0.18 -0.13 0.16 1.1 0.15 ri-score-k1/tdl-bp/autodock vina ri-score,tdl-bp,autodock vina,schrodinger protein forcefield opls3 ligand forcefield opls3 water model spc structure-based score
vxc86 Duc NguyenGuo-wei wei 33 0.04 0.13 0.05 0.18 -0.08 0.16 1.03 0.15 ri-score-k1/tdl-bp/autodock vina ri-score,tdl-bp,autodock vina,schrodinger protein forcefield opls3 ligand forcefield opls3 water model spc structure-based score
tw62k Thomas EvangelidisThomas evangelidis 33 0.29 0.12 0.42 0.16 0.44 0.16 0.77 0.11 scaffopt_ligbased_fe1 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
xbq8y Thomas EvangelidisThomas evangelidis 33 0.16 0.12 0.26 0.17 0.27 0.16 0.78 0.11 scaffopt_ligbased_fe2 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
uch2m Thomas EvangelidisThomas evangelidis 33 0.27 0.11 0.39 0.16 0.41 0.15 0.77 0.11 scaffopt_ligbased_fe3 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
47ka6 Thomas EvangelidisThomas evangelidis 33 0.21 0.11 0.3 0.16 0.35 0.15 0.77 0.11 scaffopt_ligbased_fe5 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
khqjp Thomas EvangelidisThomas evangelidis 33 0.11 0.13 0.16 0.18 0.27 0.18 0.83 0.11 scaffopt_ligbased_fe6 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
vc0p5 Thomas EvangelidisThomas evangelidis 33 0.23 0.12 0.33 0.17 0.38 0.15 0.75 0.1 scaffopt_md100ps_fe1 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
jd00r Thomas EvangelidisThomas evangelidis 33 0.18 0.12 0.21 0.17 0.28 0.16 0.79 0.1 scaffopt_md100ps_fe2 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
jk3no Thomas EvangelidisThomas evangelidis 33 0.28 0.12 0.41 0.16 0.45 0.15 0.74 0.11 scaffopt_md100ps_fe3 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
rjnyn Thomas EvangelidisThomas evangelidis 33 0.24 0.12 0.31 0.17 0.36 0.16 0.75 0.1 scaffopt_md100ps_fe5 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
feofk Thomas EvangelidisThomas evangelidis 33 0.23 0.12 0.33 0.16 0.38 0.15 0.75 0.1 scaffopt_md1ns_fe1 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
gbtke Thomas EvangelidisThomas evangelidis 33 0.16 0.13 0.2 0.18 0.28 0.16 0.79 0.1 scaffopt_md1ns_fe2 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
66qqk Thomas EvangelidisThomas evangelidis 33 0.3 0.12 0.41 0.16 0.46 0.15 0.73 0.11 scaffopt_md1ns_fe3 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
2e2e3 Thomas EvangelidisThomas evangelidis 33 0.23 0.12 0.32 0.17 0.34 0.16 0.76 0.1 scaffopt_md1ns_fe5 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
fizwc Thomas EvangelidisThomas evangelidis 33 0.23 0.12 0.33 0.17 0.38 0.16 0.75 0.1 scaffopt_md5ns_fe1 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
0s2yg Thomas EvangelidisThomas evangelidis 33 0.19 0.12 0.25 0.17 0.31 0.16 0.78 0.1 scaffopt_md5ns_fe2 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
ardvo Thomas EvangelidisThomas evangelidis 33 0.15 0.12 0.22 0.17 0.28 0.16 0.77 0.11 scaffopt_md5ns_fe3 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
bcfd0 Thomas EvangelidisThomas evangelidis 33 0.23 0.12 0.32 0.16 0.34 0.15 0.76 0.1 scaffopt_md5ns_fe5 ligprep v33013 scaffopt protein forcefield none ligand forcefield none water model none ligand-based score
8br4d Zixuan CangGuo-wei wei 33 -0.01 0.13 0.01 0.18 0.11 0.18 0.89 0.12 tml&tdl-bp/ri-score/gold/autodock-vina pqb2pqr, javaplex, r-tda, scikit-learn protein forcefield charmm ligand forcefield na water model na structure-based score
ga42p Zixuan CangGuo-wei wei 33 0.04 0.13 0.06 0.19 0.09 0.18 0.98 0.13 tml&tdl-bp/ri-score/gold/autodock-vina pqb2pqr, javaplex, r-tda, scikit-learn protein forcefield charmm ligand forcefield na water model na structure-based score
tkycg Zixuan CangGuo-wei wei 33 0.01 0.13 0.03 0.18 0.04 0.18 1 0.14 tml&tdl-bp/ri-score/gold/autodock-vina pqb2pqr, javaplex, r-tda, scikit-learn protein forcefield charmm ligand forcefield na water model na structure-based score
rck54 Zixuan CangGuo-wei wei 33 0.09 0.12 0.18 0.17 0.11 0.16 0.93 0.13 tml&tdl-bp/ri-score/gold/autodock-vina pqb2pqr, javaplex, r-tda, scikit-learn protein forcefield charmm ligand forcefield na water model na structure-based score