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Abstract
We test a range of standard implicit solvent models and protein forcefields for a set of 5 experimentally characterized, designed α-helical peptides. 65 combinations of forcefield and implicit solvent models are evaluated in >800 µs of molecular dynamics simulations. The data show that implicit solvent models generally fail to reproduce the experimentally observed secondary structure content, and none performs well for all 5 peptides. The results show that these models are not usefully predictive.
Supplementary materials
Title
Supplementary information
Description
Methods, Supplementary Results, Supplementary Figures S1 to S11 and Supplementary Table S1 (PDF)
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Title
Supplementary movie S1
Description
Trajectories of the 6 µs MD simulations of A4(K4E4)1A4(K4E4)1A4 using igb5 with ff14SB (left), igb5 with ff99SBnmr (center) and igb8 with ff14SBonlysc (right). The structures are colored by secondary structures: α-helix in blue, extended β-strand and β-bridge in green, π-helix in red, 310 helix in purple, turn in orange and coil in white.
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Title
Supplementary movie S2
Description
Trajectories of the 6 µs MD simulations of A4(K4E4)1A4(K4E4)1A4 using ff96 in combination with igb5 (left), igb7 (center) and igb8 (right). The structures are colored by secondary structures: α-helix in blue, extended β-strand and β-bridge in green, π-helix in red, 310 helix in purple, turn in orange and coil in white.
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