| (111) |
AMBER/FF99 |
CYP2C9 |
Developed within their study |
5 (multiple) |
NPT |
|
| (114) |
AMBER/FF99 |
CYP2A6, 2C9, 3A4 |
Own charge method with parameters
taken from ref (113) |
5 |
NPT |
FF99 used, missing
residues in CYP3A4 (1TQN) |
| (112) |
AMBER/FF99 |
CYP2C9, CYP19 |
refs (106),
113 Ferrous low spin state (S = 0) Fit of heme charges done at DFT (B3LYP/6-31G*) level |
10 |
NPT |
Cα RMSD plateaus in phases,
culminating at ∼4
Å DFT wave function used for RESP fitting HEME parameters not
stated, only the RESP charges |
| (128) |
CHARMM
27 |
CYP3A4 |
refs (103, 109) |
6 |
NVT |
Cα RMSD plateaus at ∼1.5 Å |
| (130) |
AMBER/FF99 |
CYP1A2, 2A6, 2C9, 2D6, 3A4 |
Developed within the
study |
10 |
NPT |
FF99 used,
missing residues in 3A4 (1TQN) Heme parameters provided |
| (140) |
GROMOS96 |
CYPC17 |
GROMOS96 |
20 |
NPT |
Cα RMSD seems high
at ∼3 Å Berendsen thermostat |
| (137) |
CHARMM 27 (protein) CHARMM 22 (heme) |
CYP3A4 |
CHARMM22 Refit of heme charges done at DFT (B3LYP/MM/LACVP)
level for sextet state |
20 |
NVT |
Cα RMSD plateaus at ∼1.5 Å Thorough,
with
a rich set of supporting materials |
| (139) |
GROMOS96 |
CYP3A4 |
– |
5 |
NPT |
Cα RMSD plateaus at ∼2.5 Å |
| (124) |
AMBER/FF03
with pi-pi stacking term modification |
CYP2C9 |
Developed within their study, but used the method of ref (110) |
5 |
NPT |
Cα RMSD plateaus at ∼2.4 Å |
| (169) |
CHARMM27 |
CYP51 |
– |
20 |
NPT |
Cα RMSD not reported |
| (115) |
AMBER/FF99SB267
|
CYP3A4 |
Heme parameters for a wide range of states developed with this
study. |
25 |
NPT |
Cα RMSD
plateaus at ∼1.7 Å |
| (122) |
OPLS |
CYP119 |
Heme parameters
from ref (268) |
200 |
NVT |
RMSD of F/G loop region
indicates a large degree of flexibility. Berendsen thermostat |
| (157) |
GROMOS 45A4 |
CYP1A2 |
Not stated. |
1 |
NPT |
|
| (158) |
AMBER/FF99 |
CYP26A1 and CYP26B1 |
Not stated |
0.5 |
NVT |
|
| (132) |
CHARM22 |
CYP101 |
Heme parameters from ref
(270) |
300 |
NPT |
Longest all-atom simulation to date |
