Chapter

New Algorithms for Macromolecular Simulation

Volume 49 of the series Lecture Notes in Computational Science and Engineering pp 263-295

Implicit Solvent Electrostatics in Biomolecular Simulation

  • Nathan A. BakerAffiliated withDept. of Biochemistry and Molecular Biophysics, Washington University
  • , Donald BashfordAffiliated withDept. of Molecular Biotechnology, St. Jude Childrens Research Hospital
  • , David A. CaseAffiliated withDept. of Molecular Biology, The Scripps Research Institute

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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