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- W2065408059 abstract "A new set of bonded potentials is introduced to model the flexibility of coarse-grained polypeptide chains. Based on a statistical analysis of known structures, the bonded potentials are sequence-dependent, and the secondary-structure propensity of each amino acid is partially reflected in the Si—Bi—Bi+1—Bi+2 pseudotorsion angle, where Si and Bi denote the side-chain and backbone beads, respectively. To stabilize the secondary structures during simulations, the bonded force field must be balanced by a simplified model of the protein hydrogen bonds, based on dipole−dipole interactions. Tested on eight polypeptides with sequence lengths ranging from 17 to 98, using 200-ns molecular dynamics simulations, the coarse-grained model yields trajectories with RMSDs ranging from 3 to 8 Å from the experimental conformations. The less-structured regions of the simulated proteins exhibit the largest-amplitude movements." @default.
- W2065408059 created "2016-06-24" @default.
- W2065408059 creator A5086614323 @default.
- W2065408059 date "2010-02-04" @default.
- W2065408059 modified "2023-10-16" @default.
- W2065408059 title "Protein Backbone Dynamics Simulations Using Coarse-Grained Bonded Potentials and Simplified Hydrogen Bonds" @default.
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- W2065408059 doi "https://doi.org/10.1021/ct900408s" @default.
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