APBS: Nanoscale Biomolecular Electrostatics Software

APBS：纳米级生物分子静电软件

• 批准号: 7163526
• 负责人: Nathan A. Baker
• 金额: $ 25.82万
• 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 2008-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7163526
• 关键词: Algorithms; Biology; Biomedical Research; Biopolymers; Charge; Code; Communities; Computer software; Development; Documentation; Electrostatics; Ensure; Equation; Feedback; Future; Genetic; Goals; Investigation; Licensing; Linux; Maintenance; Methods; Modification; Molecular; NIH Program Announcements; Pathway interactions; Process; Property; Proteomics; Range; Rate; Research; Research Support; Software Design; Time; base; design; drug discovery; improved; intermolecular interaction; macromolecule; nanoscale; open source; physical model; portability; protein structure; simulation; structural genomics

DESCRIPTION (provided by applicant): The goal of this project is to continue to enable the investigation of the electrostatic properties of macromolecules for biomedical research by supporting the maintenance and continued development of the open-source Adaptive Poisson-Boltzmann Solver (APBS) software. Among the various inter- and intermolecular interactions in biomolecules, electrostatic energetics are of special importance due to their long range and the substantial charges of biopolymer components. APBS is a free, open-source software package designed to solve the equations of continuum electrostatics for large biomolecular assemblages using new highly-scalable parallel algorithms. This software was designed "from the ground up" using modern software design methods to facilitate its modification and integration with other software packages. In order to ensure the continuing availability of APBS, we propose to ensure its suitability for both end-users and software developers in the biology community through continuing maintenance; to improve existing features based on new algorithms and user feedback; to incorporate new features based on the needs of the research community; and to expand the APBS user base by educating users, improving the efficiency and portability of the code, and facilitating interaction with other biomolecular software simulation 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（APBS）软件的维护和持续开发，继续促进生物医学研究中大分子静电特性的研究。在生物分子的各种分子间和分子间相互作用中，静电能量学因其长距离和生物聚合物成分的大量电荷而特别重要。 APBS 是一个免费的开源软件包，旨在使用新的高度可扩展的并行算法求解大型生物分子组合的连续静电方程。该软件是使用现代软件设计方法“从头开始”设计的，以方便其修改以及与其他软件包的集成。为了确保 APBS 的持续可用性，我们建议通过持续维护来确保其适用于生物学界的最终用户和软件开发人员；根据新算法和用户反馈改进现有功能；根据研究界的需求纳入新功能；通过教育用户、提高代码的效率和可移植性以及促进与其他生物分子软件模拟包的交互来扩大 APBS 用户群。