Electrostatics calculations: latest methodological advances.
Electrostatics plays a major role in the stabilization and function of biomolecules; as such, it remains a major focus of theoretical and computational studies of macromolecules. Electrostatic interactions are long range, and strongly dependent on the solvent and ions surrounding the biomolecule under study. During the past year, progress has been reported in the treatment of electrostatics in explicit and implicit solvent models. Interesting new developments of explicit solvent models include more efficient Ewald summation methods, as well as alternative approaches based on reaction field theory, periodic images and Euler summations. Implicit solvent models remain divided into those that solve the Poisson-Boltzmann equation numerically and those based on the generalized Born formalism. Both approaches are now included in molecular dynamics simulations and their accuracies may be assessed by direct comparison against experimental data. It is worth mentioning the recent development of web interfaces that facilitate access to and usage of existing tools for computing electrostatic interactions.
Koehl
Patrice
P
Department of Computer Science and Genome Center, Kemper Hall, University of California, Davis, CA 95616, USA. koehl@cs.ucdavis.edu
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D008968:Molecular Conformation; D011506:Proteins / Q000737:chemistry; D012997:Solvents / Q000737:chemistry*; D055672:Static Electricity; D013816:Thermodynamics
D011506:Proteins; D012997:Solvents