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A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation.
via PubMed: "protein structure p... by (author unknown) on May 12, 2008
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Problem is that we still have a long way to goRelated Articles A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation.
J Phys Chem B. 2008 May 10;
Authors: Shell MS, Ritterson R, Dill KA
We used replica exchange molecular dynamics (REMD) simulations to evaluate four different AMBER force fields and three different implicit solvent models. Our aim was to determine if these physics-based models captured the correct secondary structures of two alpha-helical and two beta-peptides: the 14-mer EK helix of Baldwin and co-workers, the C-terminal helix of ribonuclease, the 16-mer C-terminal hairpin of protein G, and the trpzip2 miniprotein. The different models gave different results, but generally we found that AMBER ff96 plus the implicit solvent model of Onufriev, Bashford, and Case gave reasonable structures, and is fairly well-balanced between helix and sheet. We also observed differences in the strength of ion pairing in the solvent models, we but found that the native secondary structures were retained even when salt bridges were prevented in the conformational sampling. Overall, this work indicates that some of these all-atom physics-based force fields may be good starting points for protein folding and protein structure prediction.
PMID: 18471007 [PubMed - as supplied by publisher]
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