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: 8464744
• 负责人: RAY LUO
• 金额: $ 24.9万
• 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 2015-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8464744
• 关键词: Algorithms; Area; Behavior; Binding Proteins; Charge; Communities; Complex; Computer software; Development; Drug Design; Equation; Equilibrium; Event; Hand; Lead; Licensing; Maintenance; Mediating; Methods; Modeling; Molecular; Molecular Models; Performance; Play; Right-On; Role; Solutions; Source; Structure; Surface; System; Text; Visit; Water; computer program; data structure; electric field; enzyme mechanism; improved; molecular modeling; open source; parallel computing; particle; programs; protein folding; protein misfolding; protein structure; public health relevance; salt water environment; self assembly; 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.

这些项目的GEAL项目是遏制琥珀/PBSA的开发和维护 复杂生物分子的溶液介导的遗传学和代码分析的计划 系统。生物分子通常在盐水环境中起作用，该环境具有很强的作用 关于它们的结构和功能。水具有OBOUT 88的介电常数，而 生物分子内部的二元二元常数高达2。这导致了可爱的相互作用 原子原子的收费和高含水。在动脉遥远的手上 水筛或减少了IMONG原子电荷的相互作用。水也会引起 疏水作用，水分子驱动非极性溶质的趋势。这 促进生物分子的自我组装或在 不同的生物分子。这些溶剂化效应通常是通过隐式溶解膜建模的 高性能能量学和动力学分析的方法。广泛 二手琥珀色/PBSA程序是一个用于隐含solvateon的apen源计算机程序 生物分子的处理。一个项目，我们建议改善AMBAR/PBSA计划 通过离职，偏向的名义算法并扩大其粉丝actionition性 可用的串行和并行计算平台。我们建议恶魔新的分析 模仿生物核能动力学的鲁棒建模的方法。最后，我们将扩展 软件接口访问琥珀色Cemmunity之外的更多用户。