TABI-PB 2.0: An Improved Version of the Treecode-Accelerated Boundary Integral Poisson-Boltzmann Solver
TABI-PB 2.0: An Improved Version of the Treecode-Accelerated Boundary Integral Poisson-Boltzmann Solver
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DOI：
10.1021/acs.jpcb.2c04604
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发表时间：
2022-09-01
影响因子：
3.3
通讯作者：
Krasny，Robert
中科院分区：
文献类型：
--
作者：
Wilson，Leighton;Geng，Weihua;Krasny，Robert
这项工作描述了 TABI-PB 2.0，它是树代码加速边界积分泊松-玻尔兹曼求解器的改进版本。该代码计算溶剂化生物分子分子表面上的静电势，并进一步处理产生静电溶剂化能。新的实现利用了 NanoShaper 表面三角剖分代码、节点块边界积分离散化、块预处理器以及基于重心拉格朗日插值和对偶树遍历的快速多极方法。代码的性能关键部分是在 GPU 上实现的。蛋白质 1A63 和两种病毒衣壳（Zika、H1N1）的数值结果证明了代码的准确性和效率。
This work describes TABI-PB 2.0, an improved version of the treecode-accelerated boundary integral Poisson-Boltzmann solver. The code computes the electrostatic potential on the molecular surface of a solvated biomolecule, and further processing yields the electrostatic solvation energy. The new implementation utilizes the NanoShaper surface triangulation code, node-patch boundary integral discretization, a block preconditioner, and a fast multipole method based on barycentric Lagrange interpolation and dual tree traversal. Performance-critical portions of the code were implemented on a GPU. Numerical results for protein 1A63 and two viral capsids (Zika, H1N1) demonstrate the code’s accuracy and efficiency.