MIBPB: Matched Interface and
Boundary Based Poisson-Boltzmann Solver
Software package for
the estimation of electrostatic properties of biomolecules
Online server is
located at http://weilab.math.msu.edu/MIBPB/
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
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
1.1 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.
More
information
Reference
Please acknowledge your use of MIBPB by citing:
- Duan
Chen, Zhan Chen, Changjun Chen, Weihua Geng and Guo-Wei
Wei, MIBPB: A software
package for electrostatic analysis, Journal of Computational Chemistry, 32, 756–770 (2011).
- Y.C. Zhou,
M. Feig and G.W. Wei, Highly accurate biomolecular electrostatics in continuum dielectric
environments, J. Comput. Chem. 29,
87-97 (2008).
- W.H.
Geng, S.N. Yu and G.W. Wei, Treatment of charge
singularities in implicit solvent models, J. Chem. Phys., 127, 114106
(20 pages) (2007).
- S.
N. Yu, W. H. Geng and G.W. Wei, Treatment of geometric
singularities in implicit solvent models, J. Chem. Phys., 126,
244108 (13 pages) (2007).
MIBPB is based on the MIB method mainly developed in the following
references
- S.N.
Yu and G.W. Wei, Three
dimensional matched interface and boundary (MIB) method for geometric
singularities, J. Comput. Phys. 227, 602-632 (2007).
- S. N. Yu, Y.
C. Zhou and G. W. Wei, Matched interface and
boundary (MIB) method for elliptic problems with sharp-edged interfaces,
J. Comput. Phys.224, 729-756 (2007).
- Y.C. Zhou
and G.W. Wei, On the
fictitious domain and interpolation formulations of the matched interface
and boundary (MIB) method, J. Comput. Phys.
219, 228-246 (2006).
- Y.C. Zhou,
S. Zhao, M. Feig and G. W. Wei, High order matched
interface and boundary (MIB) schemes for elliptic equations with
discontinuous coefficients and singular sources, J. Comput. Phys.,213, 1-30, (2006).
- S. Zhao and
G.W. Wei, High order
FDTD methods via derivative matching for Maxwell's equations with material
interfaces, J. Comput. Phys., 200, 60-103,
(2004).
Acknowledgment
MIBPB
software package has incorporated three important supporting packages:
- MSMS package
for the molecular surface
generation (optional)
- PDB2PQR for the pretreatment of
PDB data.
- SLATEC
for the speed-up of the algebraic equation solver
Supporting
Organizations:
Feedback
For any problem and comment, please
contact:
Guowei Wei
Department of Mathematics
Michigan State University
D301 Wells Hall
East Lansing, MI
Phone: 517 353 4689
Departmental Fax: 517 432 1562
Email: wei@math.msu.edu