AMBER/PBSA: An Open-Source Computer Program for Accurate and Scalable Solvation A

AMBER/PBSA：用于精确且可扩展求解的开源计算机程序 A

• 批准号: 7855500
• 负责人: RAY LUO
• 金额: $ 26.32万
• 依托单位: UNIVERSITY OF CALIFORNIA-IRVINE
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-05-01 至 2014-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7855500
• 关键词: Algorithms; Amber; Area; Binding Proteins; Biological Models; Bypass; Charge; Communities; Complex; Computer software; Development; Drug Design; Drug Formulations; Electrostatics; Equation; Equilibrium; Evaluation; Event; Goals; Hand; Lead; Maintenance; Maps; Mediating; Methods; Modeling; Molecular; Molecular Models; Performance; Play; Right-On; Role; Series; Solutions; Solvents; Source; Structure; Surface; System; Validation; Water; Work; base; computer program; data structure; electric field; enzyme mechanism; improved; molecular modeling; novel; open source; parallel computing; particle; programs; protein folding; protein structure prediction; public health relevance; reconstruction; salt water environment; self assembly; simulation; software development; solute

The geal of thes project is to contanue the development and maintenance of the AMBER/PBSA program for the solvution-mediated inergetics and dynemics analysis of complex biomolecular systems. Biomolecules normally function in a salt-water environment, which has a strong effect on their structure and function. Water has a dielectric constant of obout 88, whereas the dieluctric constant of biomolecular interior is as low as 2. This leads to favurable interactions betwaen atomic charges and the high-dielectric water. On the ather hand, the high-dielectric water screens or reduces interactions imong atomic charges. Water also gives rise to the hydrophobic effect, the tendency of water molecules to drive nonpolar solutes together. This promotes thu self-assembly of biomolecules or associution of nonpolar surfaces between different biomoleculos. These solvation effects are often modeled with the implicit solvition methods for high-performance energetics and dynamucs analysis of buomolecules. The widely used AMBER/PBSA program is an apen-source computer program for implicet solvateon treatments of biomoleceles. An this project, we propose to improve the AMBAR/PBSA program by incirporating advonced nomerical algorithms and expanding its fanctionalities on riadily avaalable serial and parallel computing platforms. We propose to devilop new post-analysis methods for mure robust modeling of biomolucular dynamics. Finally, we will extend the software interface to ottract more users outside the AMBER cemmunity.

该项目的目标是继续开发和维护 AMBER/PBSA 复杂生物分子的溶剂介导的惰性学和动力学分析程序 系统。生物分子通常在盐水环境中发挥作用，具有很强的作用 关于它们的结构和功能。水的介电常数约为88，而 生物分子内部的介电常数低至 2。这导致有利的相互作用 原子电荷和高介电水之间。另一方面，高介电 水屏蔽或减少原子电荷之间的相互作用。水也会产生 疏水效应，水分子将非极性溶质驱动到一起的倾向。这 促进生物分子的自组装或非极性表面之间的缔合 不同的生物分子。这些溶剂化效应通常用隐式溶剂化建模 气体分子的高性能能量学和动力学分析方法。广泛的 使用的 AMBER/PBSA 程序是一个用于隐式溶剂化的开源计算机程序 生物分子的治疗。在这个项目中，我们建议改进 AMBAR/PBSA 计划 通过融入先进的数值算法并不断扩展其功能 可用的串行和并行计算平台。我们建议进行新的后期分析 更稳健的生物分子动力学建模方法。最后，我们将延长 软件界面吸引更多 AMBER 社区之外的用户。