2004
DOI: 10.1002/prot.20033
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Exploring protein native states and large‐scale conformational changes with a modified generalized born model

Abstract: Implicit solvation models provide, for many applications, a reasonably accurate and computationally effective way to describe the electrostatics of aqueous solvation. Here, a popular analytical Generalized Born (GB) solvation model is modified to improve its accuracy in calculating the solvent polarization part of free energy changes in large-scale conformational transitions, such as protein folding. In contrast to an earlier GB model (implemented in the AMBER-6 program), the improved version does not overstab… Show more

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Cited by 2,277 publications
(2,349 citation statements)
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References 37 publications
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“…3. Normal modes and trajectories of mode displacements were additionally calculated from the same structure used in the elastic normal mode calculations using GROMACS with the CHARMM27 force field combined with the OBC (Onufriev, Bashford, Case) implicit solvent model 51 . The structure was thoroughly minimized to reach a minimum before the normal mode analysis was made in GROMACS 52 .…”
Section: Methodsmentioning
confidence: 99%
“…3. Normal modes and trajectories of mode displacements were additionally calculated from the same structure used in the elastic normal mode calculations using GROMACS with the CHARMM27 force field combined with the OBC (Onufriev, Bashford, Case) implicit solvent model 51 . The structure was thoroughly minimized to reach a minimum before the normal mode analysis was made in GROMACS 52 .…”
Section: Methodsmentioning
confidence: 99%
“…The Onufriev− Bashford−Case implicit solvent model was chosen to represent the solution environment around the protein in order to avoid possible confined aqueous volume effects and specific heat errors on the simulated structures. 5,6,41,42 Particle mesh Ewald method was used to treat the long-range interactions using a cutoff value of 25 Å. 46,47 The temperature was maintained by employing Langevin dynamics with a collision frequency of 2 ps −1 .…”
Section: ■ Methodsmentioning
confidence: 99%
“…One approach that has been widely used for the simulations of disordered proteins is the parallel tempering method. 41,42 Such simulations help to increase the conformational sampling in comparison to classical MD simulations without the application of special sampling techniques, which can be trapped in one specific potential minimum. 4−8,12,19,20,22,32−37 Using parallel tempering MD simulations, we studied the structural properties including the secondary and tertiary structures as well as the free energy landscapes of the wild-and R5A mutant-type Aβ42 peptides in an aqueous solution medium and compared these characteristics to one another.…”
Section: Aβ42 Presented In Bold: D a E F R H D S G Y E V H H Q K L Vmentioning
confidence: 99%
“…Solvent effects were modelled implicitly with the generalized Born model-II of Onufriev et al 35 , which is implemented in Amber 8. The dielectric constants of 1 and 78.5 were used for the protein interior and solvent regions, respectively.…”
Section: Generalized Born Simulationsmentioning
confidence: 99%