MIBPB: Matched Interface and Boundary Based Poisson-Boltzmann Solver

Software package for the estimation of electrostatic properties of biomolecules

 

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General Introduction

 

MIBPB is a software package for evaluating electrostatic properties of biomolecules via the solution of the Poisson-Boltzmann equation (PBE), an established two-scale model in biomolecular simulations. The PBE is one of the most popular implicit solvent models that explicitly describe atoms in biomolecules while represent interactions between molecules and solvent by a mean-field approximation. In this model, solvent is treated as a dielectric continuum, while ions within the solvent are assumed to have the Boltzmann distribution with respect to the electrostatic energy. In biological modeling and simulation, the PBE has been widely employed for various studies, including:

 

·         Solvation analysis, i.e., electrostatic salvation free energies

·         Impact of surface electrostatics in protein-protein, protein-ligand, and protein-DNA (RNA) binding

·         Binding kinetics of protein-protein, protein-ligand, and protein-DNA (RNA) interactions

·         Molecular dynamics simulation via implicit solvent approach

·         Evaluation of pKa and pH values of biomolecules

 

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Technical aspects

 

MIBPB is extremely accurate at a given grid resolution and fast at a given accuracy. It distinguishes itself from other PBE solvers by rigorously enforcing the interface flux continuity condition. The matched interface and boundary (MIB) method, an advanced mathematical technique for elliptic interface problems, is implemented in the MIBPB-I to enforce not only continuity of the solution, but also the continuity of the flux (i.e., weighted derivatives) at the dielectric interface. Both MIB and MIBPB are developed in Wei group over a few years’ time, in collaboration with a number of former and current PhD students (i.e., Dr. Shan. Zhao, Dr. Yongcheng Zhou, Dr. Sining Yu, Dr. Weihua Geng,  Mr. Duan Chen and Mr. Zhan Chen), and Dr. Michael Feig.

 

The current MIBPB is the only known PBE solver that is of second order accuracy in biomolecular context. Unlike other PB methods, MIBPB is stable for molecular surfaces and other sharp dielectric boundaries in its evaluation of electrostatic potentials and forces. This is made possible by carefully dealing with geometric singularities of the molecular surfaces in the second generation MIB based PB solver, the MIBPB-II. However, MIBPB-II cannot maintain its high accuracy when the grid size is as large as half of the atomic radius (about 0.6 angstrom for the hydrogen), due to the interference of the interface and singular charges. A regularization scheme using Green’s function method is introduced in the third generation MIB based PB solver, MIBPB-III, with which, very accurate solution of the PBE can be obtained at the grid size as large as 1.2 angstrom for proteins. The current MIBPB package is accelerated by appropriate preconditioners.

 

Currently, MIBPB solutions to both the Poisson equation and the (nonlinear) PBE are available. While the development of MIBPB based molecular dynamics (MIBPB-MD) is in progressing. A parallel MIBPB package is also under consideration. 

 

The present MIBPB package has significantly benefited from the molecular surface software package, MSMS, the PDB data preprocessing package, PDB2PQR, and the algebraic equation package, SLATEC. 

 

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More information

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Download

The current version of MIBPB can be obtained here:

·         Single-step version           Multistep version

·         All-in-one package

 

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Reference

Please acknowledge your use of MIBPB by citing:

 

MIBPB is based on the MIB method mainly developed in the following references

 

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Acknowledgment

 

MIBPB software package has incorporated three important supporting packages:

 

Supporting Organizations:

 

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Feedback

 

For any problem and comment, please contact:

 

Guowei Wei

Department of Mathematics
Michigan State University
D301 Wells Hall
East Lansing, MI 48824
Phone: 517 353 4689

Departmental Fax: 517 432 1562
Email: wei@math.msu.edu

http://www.math.msu.edu/~wei/