Development and Maintenance of the MEAD Software Suite

MEAD 软件套件的开发和维护

• 批准号: 7931261
• 负责人: DONALD E. BASHFORD
• 金额: $ 17.87万
• 依托单位: ST. JUDE CHILDREN'S RESEARCH HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-30 至 2012-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7931261
• 关键词: Algorithms; Ally; Binding; Biological; Code; Communities; Complex; Computer Systems; Computer software; Development; Documentation; Drug Interactions; Electrolytes; Electronics; Electrostatics; Environment; Enzymes; Equation; Free Energy; Freedom; Frequencies; Future; General Population; Generations; Generic Drugs; Glues; Grant; Growth; Hybrids; Individual; Internet; Language; Libraries; Licensing; Maintenance; Methods; Microscopic; Modeling; Modification; Molecular; Movement; NIH Program Announcements; Operative Surgical Procedures; Oxidation-Reduction; Performance; Pharmaceutical Preparations; Property; Proteins; Pythons; Reaction; Research; Research Personnel; Resources; Screening procedure; Solutions; Solvents; Speed; Surface; System; Techniques; Testing; Work; Writing; absorption; base; chromophore; cluster computing; computational chemistry; design; electronic structure; improved; interest; ionization; molecular mechanics; multicore processor; open source; pressure; programs; protein function; public health relevance; quantum; quantum chemistry; tool; virtual; web site

DESCRIPTION (provided by applicant): The PI has developed a software suite, called MEAD, for calculations of electrostatic properties of proteins using continuum electrostatic models. MEAD is useful for the calculation of the ionization properties of sidechains, redox potentials of redox-active proteins, energetics of enzyme mecha- nisms, stability of proteins and protein-drug interactions. The NIH program announcement PAR-08-010, "Continued Development and Maintenance of Software," calls for proposals for the development and maintenance of ex- isting software that serves a biological community of users. The proposed project will do this in several ways. (1) Combination of the program with computational chemistry software making hybrid techniques available to a broad community that were heretofore available only in the research group of the PI and collaborators. (2) Optimization of MEAD for the new multi-core processors. (3) Improvements to MEAD's object-oriented library to open up its capabilities to a wider range of programmers, including programmers who prefer to program in high-level scripting languages, particularly Python. (4) The addition of new or improved improved molecular surface and en- ergy minimization capabilities. (5) Documentation and web resources to promote the continued growth and interactivity of the MEAD user commu- nity, and to help users outside the PI's group not only to use the programs, but to use the library to develop their own customized applications. MEAD has been, and will continue to be distributed on an open-source basis. PUBLIC HEALTH RELEVANCE: The MEAD software suite calculates electrostatic effects in protein mol- ecules, helping researchers understand the function of proteins of biomed- ical interest. It is also used to calculate protein-drug interactions for "virtual screening," in which potential drug molecules are evaluated computation- ally to narrow down the number of molecules needing costly experimen- tal tests. The proposed grant will support the continued development and maintenance of MEAD.

描述（由申请人提供）：PI开发了一个软件套件，称为MEAD，用于使用连续体静电模型计算蛋白质的静电特性。MEAD可用于计算侧链的电离性质、氧化还原活性蛋白质的氧化还原电位、酶机制的能量学、蛋白质的稳定性和蛋白质-药物相互作用。NIH计划公告PAR-08-010，“软件的持续开发和维护”，要求为服务于生物用户社区的前药软件的开发和维护提出建议。拟议的项目将以几种方式做到这一点。(1)该计划与计算化学软件的结合使混合技术可用于广泛的社区，迄今为止仅在PI和合作者的研究小组中可用。(2)针对新的多核处理器优化MEAD。(3)改进MEAD的面向对象库，向更广泛的程序员开放其功能，包括喜欢用高级脚本语言（特别是Python）编程的程序员。(4)增加新的或改进的分子表面和能量最小化能力。(5)文档和网络资源，以促进MEAD用户社区的持续增长和互动，并帮助PI组以外的用户不仅使用程序，而且使用库开发自己的定制应用程序。MEAD已经并将继续在开源基础上分发。公共卫生关系：MEAD软件套件计算蛋白质分子的静电效应，帮助研究人员了解生物医学感兴趣的蛋白质的功能。它还用于计算蛋白质-药物相互作用以进行“虚拟筛选”，其中通过计算评估潜在的药物分子以缩小需要昂贵的实验测试的分子数量。拟议的赠款将支持继续发展和维护MEAD。