Development and Maintenance of the MEAD Software Suite

摘要 PI已经开发了一个软件套件，称为MEAD，用于计算 蛋白质的静电特性的连续静电模型。 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， nisms，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，“继续开发和维护 软件，”呼吁为开发和维护前- 为生物用户社区服务的软件。拟议 该项目将以几种方式做到这一点。(1)该方案与 计算化学软件使混合技术可用于 广泛的社区，迄今为止只有在研究小组 私家侦探和合作者(2)针对新型多核的MEAD优化 处理器. (3)改进MEAD的面向对象库以打开 将其功能提升到更广泛的程序员，包括程序员 他们更喜欢用高级脚本语言编程，尤其是Python。 (4)添加新的或改进的分子表面和增强剂， 能量最小化能力。(5)文档和网络资源， 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， 而是使用该库来开发他们自己的定制应用程序。米德 它已经并将继续在开放源代码的基础上分发。项目叙述（相关性） MEAD软件套件计算蛋白质分子中的静电效应， ecules，帮助研究人员了解生物医学蛋白质的功能， 有趣的兴趣它也被用来计算蛋白质-药物相互作用的“虚拟”， 筛选，”其中潜在的药物分子被评估计算- 以减少需要昂贵实验的分子数量， 谈话测试。拟议的赠款将支持继续发展， MEAD的维护。

Abstract 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. Project Narrative (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.