Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation

scientific article published on 27 January 2007

Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1021/JP066831U
P932PMC publication ID4810457
P698PubMed publication ID17256983

P2093author name stringCarlos Simmerling
Asim Okur
Viktor Hornak
Lauren Wickstrom
Daniel R Roe
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Effective Born radii in the generalized Born approximation: the importance of being perfectQ28221237
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Exploring protein native states and large-scale conformational changes with a modified generalized born modelQ29617088
Unfolded state of polyalanine is a segmented polyproline II helix.Q30341342
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Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solventQ33713877
Polyproline II structure in a sequence of seven alanine residues.Q34034318
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Hydration dynamics near a model protein surface.Q34185121
Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?Q34189756
Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins.Q34478711
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Improving implicit solvent simulations: a Poisson-centric viewQ36101076
Estimation of Absolute Free Energies of Hydration Using Continuum Methods:  Accuracy of Partial Charge Models and Optimization of Nonpolar ContributionsQ44854320
Incorporating variable dielectric environments into the generalized Born modelQ44909942
A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solutionQ46188365
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Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent modelQ47307353
Polyproline II helix is the preferred conformation for unfolded polyalanine in waterQ47715263
Investigation of Salt Bridge Stability in a Generalized Born Solvent Model.Q51295899
P433issue7
P407language of work or nameEnglishQ1860
P921main subjectbiasQ742736
P1104number of pages12
P304page(s)1846-1857
P577publication date2007-01-27
P1433published inJournal of Physical Chemistry BQ668669
P1476titleSecondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation
P478volume111

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