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      Generalized Born Implicit Solvent Models for Biomolecules

      1 , 2
      Annual Review of Biophysics
      Annual Reviews

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          Abstract

          It would often be useful in computer simulations to use an implicit description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation and can be very efficient compared to the explicit treatment of the solvent. Here, we review a particular class of so-called fast implicit solvent models, generalized Born (GB) models, which are widely used for molecular dynamics (MD) simulations of proteins and nucleic acids. These approaches model hydration effects and provide solvent-dependent forces with efficiencies comparable to molecular-mechanics calculations on the solute alone; as such, they can be incorporated into MD or other conformational searching strategies in a straightforward manner. The foundations of the GB model are reviewed, followed by examples of newer, emerging models and examples of important applications. We discuss their strengths and weaknesses, both for fidelity to the underlying continuum model and for the ability to replace explicit consideration of solvent molecules in macromolecular simulations.

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          Most cited references120

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          Quantum mechanical continuum solvation models.

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            COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient

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              How fast-folding proteins fold.

              An outstanding challenge in the field of molecular biology has been to understand the process by which proteins fold into their characteristic three-dimensional structures. Here, we report the results of atomic-level molecular dynamics simulations, over periods ranging between 100 μs and 1 ms, that reveal a set of common principles underlying the folding of 12 structurally diverse proteins. In simulations conducted with a single physics-based energy function, the proteins, representing all three major structural classes, spontaneously and repeatedly fold to their experimentally determined native structures. Early in the folding process, the protein backbone adopts a nativelike topology while certain secondary structure elements and a small number of nonlocal contacts form. In most cases, folding follows a single dominant route in which elements of the native structure appear in an order highly correlated with their propensity to form in the unfolded state.
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                Author and article information

                Journal
                Annual Review of Biophysics
                Annu. Rev. Biophys.
                Annual Reviews
                1936-122X
                1936-1238
                May 06 2019
                May 06 2019
                : 48
                : 1
                : 275-296
                Affiliations
                [1 ]Departments of Computer Science and Physics, Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24060, USA;
                [2 ]Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA;
                Article
                10.1146/annurev-biophys-052118-115325
                6645684
                30857399
                875b1d97-6a4d-4c1a-a10b-b7d72b398415
                © 2019
                History

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