APBS: NANOSCALE BIOMOLECULAR ELECTROSTATICS SOFTWARE

APBS：纳米级生物分子静电软件

• 批准号: 7625352
• 负责人: Nathan A. Baker
• 金额: $ 30.22万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-01-15 至 2013-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7625352
• 关键词: Address; Adoption; Algorithms; Automation; Biological Process; Biomedical Research; Biopolymers; Charge; Code; Communities; Complex; Computational Biology; Computer software; Data; Databases; Development; Disease; Documentation; Electrostatics; Ensure; Equation; Feedback; Funding; Genetic; Goals; Hydrogen; Hydrogen Bonding; Investigation; Licensing; Maintenance; Methods; Modeling; Molecular; Molecular Structure; Mutation; Output; Pathway interactions; Play; Preparation; Process; Property; Proteins; Proteomics; Radial; Research Personnel; Research Support; Role; Services; Structure; Time; Titrations; Update; base; design; drug discovery; improved; macromolecule; molecular scale; nanoscale; open source; physical model; protein structure; public health relevance; simulation; structural genomics

DESCRIPTION (provided by applicant): The goal of this project is to enable the investigation of the salvation and electrostatic properties of macromolecules in biomedical research by supporting the maintenance and continued development of the open-source Adaptive Poisson- Boltzmann Solver and PDB2PQR software packages. An understanding of electrostatic interactions is essential for the study of biomolecular processes. The structures of proteins and other biopolymers are being determined at an increasing rate through structural genomics and other efforts while specific linkages of these biopolymers in cellular pathways or supramolecular assemblages are being detected by genetic and proteomic studies. To integrate this information in physical models for drug discovery or other applications requires the ability to evaluate the energetic interactions within and between biopolymers. Among the various components of molecular energetic, salvation properties and electrostatic interactions are of special importance due to the long range of these interactions and the substantial charges of typical biopolymer components. APBS is a unique software package which solves the equations of continuum electrostatics for large biomolecular assemblages. This software was designed "from the ground up" using modern design principles to ensure its ability to interface with other computational packages and evolve as methods and applications change over time. The APBS code is accompanied by extensive documentation for both users and programmers and is supported by a variety of utilities for preparing calculations and analyzing results. Finally, the free, open-source APBS license ensures its accessibility to the entire biomedical community. The use of continuum salvation methods such as APBS requires accurate and complete structural data as well as force field parameters such as atomic charges and radii. Unfortunately, the limiting step in continuum electrostatics calculations is often the addition of missing atomic coordinates to molecular structures from the Protein Data Bank and the assignment of parameters to these structures. To address this problem, we have developed PDB2PQR. This server automates many of the common tasks of preparing structures for continuum salvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation. This automation allows any non-expert to convert PDB files into formats that can be used for more complex analyses. Like APBS, PDB2PQR is also distributed under an open source license to facilitate its use by biomedical researchers everywhere. PUBLIC HEALTH RELEVANCE: An understanding of electrostatic interactions is essential for the study of the biomolecular-scale processes that are fundamental to understanding basic biological processes and undertaking the rational treatment of disease. Electrostatics plays an important role in all basic molecular-scale phenomena and therefore is integral to the analysis of biomolecular structure and interactions, including the study of health-related protein mutations and design of new molecular therapies. The goal of this project is to enable the investigation of the salvation and electrostatic properties of macromolecules in biomedical re- search by supporting the maintenance and continued development of the open-source Adaptive Poisson-Boltzmann Solver and PDB2PQR software packages.

描述（由申请人提供）：该项目的目标是通过支持开源自适应泊松-玻尔兹曼求解器和 PDB2PQR 软件包的维护和持续开发，实现生物医学研究中大分子的拯救和静电特性的研究。了解静电相互作用对于研究生物分子过程至关重要。通过结构基因组学和其他努力，蛋白质和其他生物聚合物的结构正在以越来越快的速度被确定，而这些生物聚合物在细胞途径或超分子组合中的特定联系正在通过遗传和蛋白质组学研究来检测。要将这些信息整合到药物发现或其他应用的物理模型中，需要能够评估生物聚合物内部和之间的能量相互作用。在分子能量的各种成分中，拯救特性和静电相互作用特别重要，因为这些相互作用的范围很长并且典型的生物聚合物成分具有大量电荷。 APBS 是一个独特的软件包，可求解大型生物分子组合的连续静电方程。该软件是使用现代设计原理“从头开始”设计的，以确保其能够与其他计算包交互，并随着方法和应用程序随时间的变化而发展。 APBS 代码附有供用户和程序员使用的大量文档，并得到各种用于准备计算和分析结果的实用程序的支持。最后，免费、开源的 APBS 许可证确保整个生物医学界都可以使用它。使用APBS等连续介质拯救方法需要准确完整的结构数据以及原子电荷和半径等力场参数。不幸的是，连续静电计算的限制步骤通常是将缺失的原子坐标添加到蛋白质数据库中的分子结构中，并将参数分配给这些结构。为了解决这个问题，我们开发了PDB2PQR。该服务器可自动执行许多常见任务，即为连续介质拯救计算准备结构以及许多其他类型的生物分子结构建模、分析和模拟。这种自动化允许任何非专家将 PDB 文件转换为可用于更复杂分析的格式。与 APBS 一样，PDB2PQR 也是在开源许可下分发的，以方便世界各地的生物医学研究人员使用它。公共健康相关性：了解静电相互作用对于研究生物分子尺度过程至关重要，而生物分子尺度过程是理解基本生物过程和合理治疗疾病的基础。静电在所有基本分子尺度现象中发挥着重要作用，因此是生物分子结构和相互作用分析不可或缺的一部分，包括与健康相关的蛋白质突变的研究和新分子疗法的设计。该项目的目标是通过支持开源自适应泊松-玻尔兹曼求解器和 PDB2PQR 软件包的维护和持续开发，实现生物医学研究中大分子的拯救和静电特性的研究。