The generalized Born model: its foundation, applications, and limitations

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The generalized Born (GB) approximation is introduced in the context of the implicit solvent framework. The physical foundations of the model and its derivation from the underlying Poisson-Boltzmann model are presented in detail. Examples of various flavors of the basic GB model are discussed, followed by examples of recent applications of the approximation in molecular modeling and simulations. Several practical issues such as the accuracy/speed trade-offs, and specific computational advantages of GB-based molecular simula-tions relative to those based on the explicit solvent model are explored. Limitations of the model and future methodological directions and challenges are discussed.

Author-supplied keywords

  • generalized born
  • implicit solvent
  • molecular simulations
  • poisson-boltzmann

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  • Alexey Onufriev

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