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放源码的自适应泊松-玻尔兹曼解算器(APBS)软件的维护和继续开发，继续使生物医学研究中的大分子静电特性的研究成为可能。在生物大分子中的各种分子间和分子间相互作用中，静电能学因其射程远和生物聚合物组分的大量电荷而具有特别重要的意义。APBS是一个免费的、开源的软件包，旨在使用新的高度可扩展的并行算法来求解大型生物分子组装的连续统静电方程。这款软件是使用现代软件设计方法“从头开始”设计的，以便于修改和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合生物界的最终用户和软件开发人员；根据新算法和用户反馈来改进现有功能；根据研究社区的需要加入新功能；以及通过教育用户、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互动来扩大APBS的用户基础。