AutoDock Software Development and Maintenance

AutoDock软件开发与维护

• 批准号: 8537472
• 负责人: ARTHUR J. OLSON
• 金额: $ 49.18万
• 依托单位: SCRIPPS RESEARCH INSTITUTE, THE
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-01-01 至 2016-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8537472
• 关键词: Address; Architecture; Archives; Binding; Biological; Biology; Biomedical Research; Chemicals; Code; Communities; Complex; Computer software; Data; Databases; Development; Docking; Documentation; Drug Design; Environment; FDA approved; Free Energy; Funding; Future; Goals; Imagery; Internet; Laboratories; Language; Learning; Libraries; Licensing; Ligands; Maintenance; Medical Research; Methods; Modeling; Molecular; Molecular Models; Performance; Pharmaceutical Preparations; Pharmacologic Substance; Positioning Attribute; Process; Proteins; Pythons; Recording of previous events; Reproducibility; Research; Research Personnel; Scientist; Screening Result; Software Engineering; Specialist; Structure; Techniques; Writing; base; clinical practice; computer code; computer program; design; drug discovery; experience; flexibility; graphical user interface; improved; interest; interoperability; molecular modeling; open source; platform-independent; programs; receptor; screening; software development; tool; usability; virtual

DESCRIPTION (provided by applicant): The AutoDock suite of programs are widely distributed community codes, used by a broad base of biomedical researchers for the prediction of biomolecular interactions and the screening of chemical compound libraries in the process of drug discovery. AutoDock was initially developed 21 years ago, to solve the flexible ligand- protein docking problem. In the intervening years both the user community and the AutoDock suite have significantly expanded. AutoDock and AutoDock Vina are now distributed under open source licenses; AutoDock is currently the world's most widely used and cited molecular docking program. Critical funding is sought to support the growing user community and to further develop AutoDock software capabilities. We are proposing to extend the usefulness, usability and maintainability of the AutoDock software, and to enhance the interactions between the users and developers by further development of the codes, utilizing contemporary software engineering practices. Our experience with the object-oriented high-level language Python has shown us that an agile, component-based, approach to software development can produce code that is easily extensible, inter-operable, maintainable, and platform independent. Computationally intensive components will be written in C or C++ and integrated with Python wrappers. Our goals for the continued development and maintenance of the AutoDock suite are to expand its usefulness, its usability and its maintainability, within an evolvable software platform, for the broad diversity of its users. In order to achieve these goals, we propose the following three specific aims that will target utility, usability and community support: 1. Utility Expand the capabilities of the AutoDock software and associated methods, to include: methods for enhanced performance; scoring function enhancements; and improved methods for pre-processing and analysis through new software development and integration of external methods 2. Usability. Develop integration-layer architecture and an AutoDock Applications Manager (ADAM) software to enhance interoperability with external methods and to facilitate the design, implementation, and archiving and reproducibility of docking and virtual screening computations. We will also develop a unified ADAM Graphical User Interface and visualization environment for docking and virtual screening, with turnkey, wizard-like interfaces for novice users and interactive tools for problem specification and analysis of virtual screening results 3. Community Support. Continue and enhance AutoDock community interaction and Internet content to strengthen user support, contributed open-source development, software dissemination, tutorials, and documentation.

描述（由申请人提供）：程序套件是广泛分布的社区代码，由广泛的生物医学研究人员用于预测生物分子相互作用和在药物发现过程中筛选化学复合库的筛选。 Autodock最初是在21年前开发的，目的是解决柔性配体蛋白对接问题。在随后的几年中，用户社区和Autock Suite都大大扩展。 Autodock和Autodock Vina现在在开源许可下分发； Autodock目前是世界上最广泛使用和引用的分子对接计划。寻求关键的资金来支持不断增长的用户社区并进一步发展自动售货机软件功能。我们建议通过使用当代软件工程实践的进一步开发代码来扩展自动售货软件的有用性，可用性和可维护性，并通过进一步开发代码来增强用户和开发人员之间的交互。我们在面向对象的高级语言python上的经验向我们表明，一种基于组件的敏捷，基于组件的方法可以生成易于扩展，可互操作，可维护，可维护和平台独立的代码。计算密集型组件将用C或C ++编写，并与Python包装纸集成。 我们在持续开发和维护Autodock Suite的目标是扩大其实用性，其可用性和可维护性，在可发展的软件平台内，以实现其用户的广泛多样性。为了实现这些目标，我们提出以下三个特定目标，这些目标将针对实用程序，可用性和社区支持：1。公用事业扩展了自动售货软件和相关方法的功能，包括：增强性能的方法；评分功能增强；以及通过新的软件开发和外部方法的集成2。可用性进行预处理和分析的改进方法。开发集成层架构和Autodock应用程序管理器（ADAM）软件，以增强与外部方法的互操作性，并促进对接和虚拟筛选计算的设计，实现以及归档和可重复性。我们还将开发一个统一的ADAM图形用户界面和可视化环境，以进行对接和虚拟筛选，并具有针对新手用户的Turnkey，类似向导的接口以及用于问题规范的交互式工具，并分析虚拟筛选结果3。 社区支持。继续并增强自动售货社区的互动和互联网内容，以增强用户支持，贡献开源开发，软件传播，教程和文档。