MIBPB: a software package for electrostatic analysis.
MIBPB: a software package for electrostatic analysis.
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DOI：
10.1002/jcc.21646
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发表时间：
2011-03
影响因子：
3
通讯作者：
Wei, Guo-Wei
中科院分区：
文献类型：
--
作者：
Chen, Duan;Chen, Zhan;Chen, Changjun;Geng, Weihua;Wei, Guo-Wei
泊松 - 玻尔兹曼方程（PBE）是生物分子静电分析的一个成熟模型。在过去的二十年中，开发用于求解PBE的先进计算技术一直是一个重要课题。本文介绍了一个基于匹配界面和边界（MIB）的PBE软件包，即MIBPB求解器，用于静电分析。MIBPB有一个独特的特点，它是第一个基于界面技术的PBE求解器，能够严格满足生物分子和溶剂之间的介电界面处的解和通量连续性条件。对于可能具有棘手几何奇异性的蛋白质分子表面，MIB方案使MIBPB成为迄今为止唯一能够实现二阶收敛的现有PBE求解器，即当网格尺寸减半时，精度提高四倍。MIBPB方法还配备了狄氏 - 诺伊曼映射（DNM）技术，该技术构建了一种格林函数方法来解析生物分子中的奇异电荷分布，以便在粗至1埃的网格上获得可靠的解——而其他传统的PB求解器通常需要0.25埃的网格才能达到类似的可靠性水平。本研究通过利用克雷洛夫子空间（KS）技术进一步加快了由MIBPB产生的线性方程组的收敛速度。通过使用适当的克雷洛夫子空间求解器和预处理器组合，显著降低了MIBPB矩阵的条件数。MIBPB软件包中的线性和非线性PBE求解器分别通过蛋白质 - 溶剂溶剂化能计算以及盐对蛋白质 - 蛋白质结合能影响的分析进行了测试。
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 paper 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, i.e., the accuracy increases four times when the mesh size is halved. The MIBPB method is also equipped with a Dirichlet-to-Neumann mapping (DNM) technique, that builds a Green's function approach to analytically resolve the singular charge distribution in biomolecules in order to obtain reliable solutions at meshes as coarse as 1Å — while it usually takes other traditional PB solvers 0.25Å to reach similar level of reliability. The present work further accelerates the rate of convergence of linear equation systems resulting from the MIBPB by utilizing the Krylov subspace (KS) techniques. Condition numbers of the MIBPB matrices are significantly reduced by using appropriate Krylov subspace solver and preconditioner combinations. Both linear and nonlinear PBE solvers in the MIBPB package are tested by protein-solvent solvation energy calculations and analysis of salt effects on protein-protein binding energies, respectively.
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影响因子：
6.1
作者：
CONNOLLY, ML
通讯作者：
CONNOLLY, ML
影响因子：
3.4
作者：
Dong, F;Vijayakumar, M;Zhou, HX
通讯作者：
Zhou, HX
影响因子：
3
作者：
BROOKS, BR;BRUCCOLERI, RE;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
3.3
作者：
Dominy, BN;Brooks, CL
通讯作者：
Brooks, CL
影响因子：
3.3
作者：
Chen, Jianhan;Brooks, Charles L., III
通讯作者：
Brooks, Charles L., III