Development and Maintenance of the MEAD Software Suite

描述(由申请人提供)：PI已经开发了一套软件，称为MEAD，用于使用连续统静电模型计算蛋白质的静电性质。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势、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社区的现有软件的开发和维护提出建议。拟议的项目将通过几种方式做到这一点。(1)将该程序与计算化学软件相结合，使迄今为止仅在PI及其合作者的研究小组中才能获得的杂交技术可供广大社区使用。(2)针对新型多核处理器的MEAD优化。(3)改进Mead的面向对象的库，向更广泛的程序员开放其功能，包括更喜欢使用高级脚本语言编程的程序员，特别是Python。(4)添加新的或改进的改进的分子表面和能量最小化能力。(5)文件和网络资源，以促进Mead用户社区的持续增长和互动，并帮助PI小组以外的用户不仅使用这些程序，而且利用图书馆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分发。与公共健康相关：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医学感兴趣的蛋白质的功能。它还被用来计算蛋白质与药物的相互作用，以进行“虚拟筛选”，即对潜在的药物分子进行计算评估，以缩小需要进行昂贵实验测试的分子数量。拟议拨款将支持米阿德机场的继续发展和维护。

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.