PB-AM：一个开源的、完全解析的线性Poisson-Boltzmann解算器
PB-AM: An Open-Source, Fully Analytical Linear Poisson-Boltzmann Solver
摘要：
我们提出了开源分布式软件包泊松-玻尔兹曼分析方法（PB-AM），完全解析解的线性泊松玻尔兹曼方程，分子表示为非重叠的球形腔。PB-AM软件包包括使用VMD生成适合于可视化的输出文件，VMD是一种布朗动力学方案，使用周期性边界条件来模拟动力学，能够指定对接标准，并提供两种不同的动力学方案来评估生物分子缔合速率常数。由于PB-AM完整而准确地定义了互极化，因此可以将其重构为多体扩展以探索2-和3-体极化。此外，该软件已被集成到自适应泊松-玻尔兹曼解算器（APBS）软件包，使其更容易为更熟悉APBS框架的科学家，教育工作者和学生群体所使用。
英文摘要：
We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation, for molecules represented as non-overlapping spherical cavities. The PB-AM software package includes the generation of outputs files appropriate for visualization using VMD, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmann Solver (APBS) software package to make it more accessible to a larger group of scientists, educators and students that are more familiar with the APBS framework.
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