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Implicit Solvent Electrostatics in Biomolecular Simulation

  • Nathan A. Baker
  • Donald Bashford
  • David A. Case
Part of the Lecture Notes in Computational Science and Engineering book series (LNCSE, volume 49)

Abstract

We give an overview of how implicit solvent models are currently used in protein simulations. The emphasis is on numerical algorithms and approximations: since even folded proteins sample many distinct configurations, it is of considerable importance to be both accurate and efficient in estimating the energetic consequences of this dynamical behavior. Particular attention is paid to calculations of pH-dependent behavior, as a paradigm for the analysis of electrostatic interactions in complex systems.

Key words

Electrostatics biomolecular simulation implicit solvent continuum solvent Poisson-Boltzmann Generalized Born 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Nathan A. Baker
    • 1
  • Donald Bashford
    • 2
  • David A. Case
    • 3
  1. 1.Dept. of Biochemistry and Molecular BiophysicsWashington UniversitySt. LouisUSA
  2. 2.Dept. of Molecular BiotechnologySt. Jude Childrens Research HospitalMemphisUSA
  3. 3.Dept. of Molecular BiologyThe Scripps Research InstituteLa JollaUSA

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