Development and Maintenance of the MEAD Software Suite

描述（由申请人提供）：PI开发了一个名为MEAD的软件套件，用于使用连续介质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与药物的相互作用。美国国立卫生研究院项目公告PAR-08-010，“软件的持续开发和维护”，呼吁为服务于生物用户群体的现有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)将该程序与计算化学软件相结合，使混合技术能够为广泛的社区所使用，而这些技术迄今仅在PI和合作者的研究小组中可用。(2)新型多核处理器的MEAD优化。(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编程的程序员，特别是Python。(4)增加新的或改进的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性，并帮助PI组之外的用户不仅使用程序，而且使用库开发他们自己的定制应用程序。MEAD已经并将继续在开源的基础上发布。公共卫生相关性：MEAD软件套件计算蛋白质分子中的静电效应，帮助研究人员了解生物组学感兴趣的蛋白质的功能。它也被用于计算“虚拟筛选”中的蛋白质-药物相互作用，其中潜在的药物分子被计算评估，以缩小需要昂贵的实验测试的分子数量。拟议的拨款将支持MEAD的持续发展和维护。

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.