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We find that when using GB\/SA: (<jats:italic>i<\/jats:italic>) A<jats:sub>21<\/jats:sub>is predicted to be more helical than the F<jats:sub>s<\/jats:sub>peptide at all temperatures; (<jats:italic>ii<\/jats:italic>) the native structure of the F<jats:sub>s<\/jats:sub>peptide is predicted to be a helical bundle instead of a single helix; and (<jats:italic>iii<\/jats:italic>) the persistence length and most probable end-to-end distance are too large in the unfolded state when compared against the explicit solvent simulations. We find that the potential of mean force in the \u03d5\u03c8 plane is markedly different in the two solvents, making the two simulated peptides respond differently when the backbone torsions are perturbed. A fit of the temperature melting curves obtained in these simulations to a Lifson\u2013Roig model finds that the GB\/SA model has an unphysically large nucleation parameter, whereas the explicit solvent model produces values similar to experiment.<\/jats:p>","DOI":"10.1073\/pnas.2232868100","type":"journal-article","created":{"date-parts":[[2003,11,25]],"date-time":"2003-11-25T20:59:06Z","timestamp":1069793946000},"page":"13934-13939","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":244,"title":["Simulation of the folding equilibrium of \u03b1-helical peptides: A comparison of the generalized Born approximation with explicit solvent"],"prefix":"10.1073","volume":"100","author":[{"given":"Hugh","family":"Nymeyer","sequence":"first","affiliation":[{"name":"Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, T10 MS K710, Los Alamos, NM 87545"}]},{"given":"Angel E.","family":"Garc\u00eda","sequence":"additional","affiliation":[{"name":"Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, T10 MS K710, Los Alamos, NM 87545"}]}],"member":"341","published-online":{"date-parts":[[2003,11,14]]},"reference":[{"key":"e_1_3_2_1_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja00172a038"},{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(19990501)35:2<173::AID-PROT4>3.0.CO;2-2"},{"key":"e_1_3_2_3_2","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1002\/prot.10248","volume":"50","year":"2003","unstructured":"Wang, T. & Wade, R. 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