MIBPB: A software package for electrostatic analysis

: The Poisson–Boltzmann equation (PBE) is an established model for the electrostatic analysis of biomolecules. The development of advanced computational techniques for the solution of the PBE has been an important topic in the past two decades. This article presents a matched interface and boundary (MIB)-based PBE software package, the MIBPB solver, for electrostatic analysis. The MIBPB has a unique feature that it is the first interface technique-based PBE solver that rigorously enforces the solution and flux continuity conditions at the dielectric interface between the biomolecule and the solvent. For protein molecular surfaces, which may possess troublesome geometrical singularities, the MIB scheme makes the MIBPB by far the only existing PBE solver that is able to deliver the second-order convergence, that is, the accuracy increases four times when the mesh size is halved. The MIBPB method is also equipped with a Dirichlet-toNeumannmappingtechniquethatbuildsaGreen’sfunctionap...

• Type: Journal
• Year: 2011
• Where: JCC
• Authors: Duan Chen, Zhan Chen, Changjun Chen, Weihua Geng, Guo-Wei Wei
• Keywords: Electrostatic Analysis, Interface Technique-based Pbe, JCC 2011, PBE Software Package