js3r3 |
Bogdan Iorga | Bogdan 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 Zou | Xiaoqin 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 Wingert | Carlos 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 Wingert | Carlos 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 Nguyen | Guo-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 Nguyen | Guo-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 Nguyen | Guo-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 Nguyen | Guo-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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Evangelidis | Thomas 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 Cang | Guo-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 Cang | Guo-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 Cang | Guo-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 Cang | Guo-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 |