SDPBS Web Server for Calculation of
Electrostatics of Ionic Solvated Biomolecules

Jiang, Yi; Xie, Yang; Ying, Jinyong; Xie, Dexuan; Yu, Zeyun

doi:10.1515/mlbmb-2015-0011

Cited by 7 publications

(10 citation statements)

References 54 publications

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“…Furthermore, the adaptive FEM developed by Holst et al has tackled some of the most important issues of the PB equation [28,29,27,30,31]. In addition, the SDPBS and SMPBS web servers developed by Xie et al for solving the size-modified PB equation have performed fast and efficiently [32,33,34,35,36].…”

Section: Previous Workmentioning

confidence: 99%

A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models

Quan¹,

Stamm²,

Maday³

2019

SIAM J. Sci. Comput.

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In this paper, a domain decomposition method for the Poisson-Boltzmann (PB) solvation model that is widely used in computational chemistry is proposed. This method, called ddLPB for short, solves the linear Poisson-Boltzmann (LPB) equation defined in R 3 using the van der Waals cavity as the solute cavity. The Schwarz domain decomposition method is used to formulate local problems by decomposing the cavity into overlapping balls and only solving a set of coupled sub-equations in balls. A series of numerical experiments is presented to test the robustness and the efficiency of this method including the comparisons with some existing methods. We observe exponential convergence of the solvation energy with respect to the number of degrees of freedom which allows this method to reach the required level of accuracy when coupling with quantum mechanical descriptions of the solute.

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Section: Previous Workmentioning

confidence: 99%

A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models

Quan¹,

Stamm²,

Maday³

2019

SIAM J. Sci. Comput.

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“…A brief description on the usages of our mesh parameters has been given in Ref. [ ]. Further guidance and usage details can be found in Ref.…”

Section: Smpbe Definition and Applicationsmentioning

confidence: 99%

“…We began web server development about one year ago, releasing the PBE web server SDPBS, which has been moved to a new URL: http://sdpbs.math.uwm.edu. Here, we developed a visualization tool based on JSmol (or Jmol http://jmol.sourceforge.net / )—one of most widely used tools to support three dimensional visualization of molecular structures of biomolecules and chemical compounds.…”

Section: Introductionmentioning

confidence: 99%

SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson‐Boltzmann equation

2017

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SMPBS (Size Modified Poisson-Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson-Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson-Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a PBE web server. SMPBS is designed with a dynamic, mobile-friendly user interface, and features easily accessible help text, asynchronous data submission, and an interactive, hardware-accelerated molecular visualization viewer based on the 3Dmol.js library. In particular, the viewer allows computed electrostatics to be directly mapped onto an irregular triangular mesh of a molecular surface. Due to this functionality and the fast SMPBE finite element solvers, the web server is very efficient in the calculation and visualization of electrostatics. In addition, SMPBE is reconstructed using a new objective electrostatic free energy, clearly showing that the electrostatics and ionic concentrations predicted by SMPBE are optimal in the sense of minimizing the objective electrostatic free energy. SMPBS is available at the URL: smpbs.math.uwm.edu © 2017 Wiley Periodicals, Inc.

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“…The Poisson–Boltzmann equation (PBE) is one of the widely used dielectric continuum models for computing the electrostatics of a biomolecule surrounded by a salt solution due to the popularity of several PBE software packages, such as DelPhi, UHBD, APBS, PBSA, and PBEQ as well as the recent software packages MIBPB and SDPBS . However, for such approach to work for modeling of ion channels on a biological membrane, such as VDAC on OMM, the PBE and its software packages need to be significantly modified to address the additional modeling and numerical solver challenges due to the geometric complexity of a transmembrane channel protein and solvent that is a mixture of many ionic species.…”

Section: Introductionmentioning

confidence: 99%

“…Numerically speaking, the governing equations for the current PBE‐based ion channel models were solved directly without using any solution decomposition reformulation, as was done in Reference to deal with the singularity difficulties caused by the atomic charges of an ion channel molecule. To the best of our knowledge, there are no ion size‐modified PBE‐based ion channel models in the literature that work for a solution of multiple ionic species, even though ion size effects have been known to be important, especially for the calculation of ionic concentrations …”

Section: Introductionmentioning

confidence: 99%

A size‐modified poisson–boltzmann ion channel model in a solvent of multiple ionic species: Application to voltage‐dependent anion channel

2019

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We present a new size‐modified Poisson–Boltzmann ion channel (SMPBIC) model and use it to calculate the electrostatic potential, ionic concentrations, and electrostatic solvation free energy for a voltage‐dependent anion channel (VDAC) on a biological membrane in a solution mixture of multiple ionic species. In particular, the new SMPBIC model adopts a membrane surface charge density and a natural Neumann boundary condition to reflect the charge effect of the membrane on the electrostatics of VDAC. To avoid the singularity difficulties caused by the atomic charges of VDAC, the new SMPBIC model is split into three submodels such that the solution of one of the submodels is obtained analytically and contains all the singularity points of the SMPBIC model. The other two submodels are then solved numerically much more efficiently than the original SMPBIC model. As an application of this SMPBIC submodel partitioning scheme, we derive a new formula for computing the electrostatic solvation free energy. Numerical results for a human VDAC isoform 1 (hVDAC1) in three different salt solutions, each with up to five different ionic species, confirm the significant effects of membrane surface charges on both the electrostatics and ionic concentrations. The results also show that the new SMPBIC model can describe well the anion selectivity property of hVDAC1, and that the new electrostatic solvation free energy formula can significantly improve the accuracy of the currently used formula. © 2019 Wiley Periodicals, Inc.

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SDPBS Web Server for Calculation of Electrostatics of Ionic Solvated Biomolecules

Cited by 7 publications

References 54 publications

A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models

A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models

SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson‐Boltzmann equation

A size‐modified poisson–boltzmann ion channel model in a solvent of multiple ionic species: Application to voltage‐dependent anion channel

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