Saturday, September 21, 2013

Force-field dependent secondary structure preferences

Weblogo representations of the per-residue secondary structure preferences (as produced by STRIDE) for folding simulations of the α-Lactalbumin-derived peptide studied in this paper. Results from seven force fields are shown. The experimental NMR results indicate a mostly 310-helical N-terminal part (residues 3-6) with an occupancy of ~50%, and a completely disordered C-terminus. The symbols in the weblogo diagrams are G => 310 helix, H => α helix, T => turn, C => random coil, E => extended. The force fields are CHARMM22, OPLSaa, AMBER ff12SB, AMBER ff99SB, and three variants of AMBER ff99SB (99SB-ILDN-NMR, 99SB-ILDN, 99SB-STAR-ILDN). It does look like a clear take-home message is present in these diagrams...

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