Journal for Biophysical Chemistry
Table 1 A qualitative comparison of FF performance, comparing experimentally observed behavior
Performance consideration (experimental finding) | Estimation of performance | ||
|---|---|---|---|
CHARMM22 | AMBER94 | OPLS-AA | |
LKβ7s in solution adopt a random coil conformation | + | − | + |
LKβ7s interact with (adsorb to) the CH3-SAM | ++ | ++ | ++ |
LKβ7s form β-strands when adsorbed to the CH3-SAM | ++ | −− | − |
LKβ7s form β-sheet when adsorbed to the CH3-SAM | ++ | −− | − |
LKβ7s oriented LEU-down when adsorbed to the CH3-SAM | ++ | + | ++ |
LKβ7s interact with (adsorbed to) the COOH-SAM | ++ | ++ | ++ |
LKβ7s form β-strands in the presence of the COOH-SAM | + | −− | − |
LKβ7s form β-sheet when adsorbed to the COOH-SAM | −− | −− | −− |
LKα14 in solution remains α-helical | ++ | ++ | − |
LKα14s interact with (adsorb to) the CH3-SAM surface | ++ | ++ | ++ |
LKα14 remains α-helical when adsorbed to CH3-SAM | ++ | + | − |
LKα14 oriented LEU-down when adsorbed to CH3-SAM | ++ | ++ | ++ |
LKα14s interact with (adsorbed to) the COOH-SAM surface | ++ | ++ | ++ |
LKα14 remains α-helical when adsorbed to COOH-SAM | + | + | − |
LKα14 oriented LYS-down when adsorbed to COOH-SAM | ++ | ++ | ++ |