Bajaj, Chandrajit; Chen, Shun-Chuan; Rand, Alexander An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics. (English) Zbl 1227.92005 SIAM J. Sci. Comput. 33, No. 2, 826-848 (2011). Summary: In order to compute the polarization energy of biomolecules, we describe a boundary element approach to solving the linearized Poisson-Boltzmann equation. Our approach combines several important features, including the derivative boundary formulation of the problem and a smooth approximation of the molecular surface based on the algebraic spline molecular surface. State of the art software for numerical linear algebra and a kernel independent fast multipole method is used for both simplicity and efficiency of our implementation. We perform a variety of computational experiments, testing our method on a number of actual proteins involved in molecular docking and demonstrating the effectiveness of our solver for computing molecular polarization energy. Cited in 17 Documents MSC: 92C05 Biophysics 92C40 Biochemistry, molecular biology 65N38 Boundary element methods for boundary value problems involving PDEs 35Q92 PDEs in connection with biology, chemistry and other natural sciences Software:F2Dock; MolEnergy; PDB2PQR; TexMol; APBS; PETSc PDFBibTeX XMLCite \textit{C. Bajaj} et al., SIAM J. Sci. Comput. 33, No. 2, 826--848 (2011; Zbl 1227.92005) Full Text: DOI