APBS: Nanoscale Biomolecular Electrostatics Software

APBS：纳米级生物分子静电软件

• 批准号: 8503329
• 负责人: Nathan A. Baker
• 金额: $ 44.85万
• 依托单位: BATTELLE PACIFIC NORTHWEST LABORATORIES
• 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 2017-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8503329
• 关键词: Address; Adoption; Algorithms; Biomedical Research; Biopolymers; Charge; Code; Communities; Computational Biology; Computer software; Data; Databases; Development; Documentation; Electrostatics; Ensure; Equation; Feedback; Funding; Genetic; Goals; Health; Hydrogen Bonding; Imagery; 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; Solutions; Structure; Time; Titrations; Update; base; design; drug discovery; improved; macromolecule; molecular scale; nanoscale; open source; physical model; protein structure; public health relevance; simulation; simulation software; structural genomics

DESCRIPTION (provided by applicant): The goal of this project is to enable the investigation of the solvation 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 energetics, solvation 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 solvation methods such as APBS requires accurate and complete structural data as well as force field parameters such as atomic charges and radii. PDB2PQR provides a software solution for such parameterization as well as biomolecular titration state assignment and visualization capability to support use by researchers with a wide range of expertise.

描述（由申请人提供）：该项目的目标是通过支持开源自适应Poisson-Boltzmann Solver和PDB 2 PQR软件包的维护和持续开发，来调查生物医学研究中大分子的溶剂化和静电性质。静电相互作用的理解是必不可少的生物分子过程的研究。蛋白质和其他生物聚合物的结构正在通过结构基因组学和其他努力以越来越快的速度确定，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。为了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。在分子能量学的各个组成部分中，溶剂化性质和静电相互作用具有特别重要的意义，因为这些相互作用的范围很长，而且典型的生物聚合物组分具有大量电荷。APBS是一个独特的软件包，它解决了大的生物分子组装的连续静电方程。该软件是使用现代设计原理“从头开始”设计的，以确保其与其他计算软件包接口的能力，并随着方法和应用程序的不断变化而发展。APBS代码附带了大量的文档，供用户和程序员使用，并得到各种实用程序的支持，用于准备计算和分析结果。最后，免费、开源的APBS许可证确保了整个生物医学社区的可访问性。使用连续溶剂化方法，如APBS，需要准确和完整的结构数据以及力场参数，如原子电荷和半径。PDB 2 PQR为这种参数化以及生物分子滴定状态分配和可视化功能提供了软件解决方案，以支持具有广泛专业知识的研究人员使用。