Development and Maintenance of the MEAD Software Suite

MEAD 软件套件的开发和维护

• 批准号: 8197630
• 负责人: DONALD E. BASHFORD
• 金额: $ 24.7万
• 依托单位: ST. JUDE CHILDREN'S RESEARCH HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-12-01 至 2013-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8197630
• 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; 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; abstracting; base; chromophore; cluster computing; computational chemistry; design; electronic structure; enzyme mechanism; improved; interest; ionization; molecular mechanics; multicore processor; open source; operation; pressure; programs; protein function; quantum; quantum chemistry; simulation; tool; virtual; web site

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.

摘要