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ABI Sustaining: Maintaining CHARMM-GUI to Support the Biomolecular Modeling and Simulation Community

ABI 维持：维护 CHARMM-GUI 以支持生物分子建模和模拟社区

基本信息

批准号：
1660380
负责人：
Wonpil Im
金额：
$ 65.93万
依托单位：
Lehigh University
依托单位国家：
美国
项目类别：
Continuing Grant
财政年份：
2017
资助国家：
美国
起止时间：
2017-08-01 至 2022-07-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1660380&HistoricalAwards=false
关键词：
ABI Sustaining Maintaining CHARMM GUI

项目摘要

Researchers who study how biomolecules flex or shift shape over time use very sophisticated algorithms as tools to understand different aspects of structure, motion and interaction. These tools are part of larger software applications that capture how the whole system behaves, including atoms and molecules that are in both the environment and the biomolecules. As researchers model larger volumes with more components, over longer study intervals, keeping track of all the elements in the system and their properties is becoming a major hurdle, even for relatively well-experienced computational biologists. The grand challenge is to maintain accuracy and reproducibility while efficiently carrying out these complex simulations in order to solve practical problems. The goal of this project is to assist two classes of researchers: experts who know how to set up the conditions and want to save and share them, and non-experts who need guidance in setting up all of the inputs and perhaps some help with interpreting the results. These challenges have been addressed by CHARMM-GUI, in that users can interactively set up complex biomolecular systems and easily understand what files must be input in order to carry out state-of-the-art biomolecular simulations. The interface is not limited to the CHARMM simulation package, despite the name, but also encompasses GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. This project aims to maintain the unique scope of the CHARMM-GUI interface application while improving the consistency of the code base to make it easier to maintain the tool going forward, and to make it easier to add new functionality that works correctly by including test suites. The project's overarching goal is to help students and researchers carry out innovative and novel biomolecular modeling and simulation research to acquire novel insight into structures, dynamics, and underlying mechanisms for the biomolecular systems of interest through availability of an excellent tool, excellent documentation with tutorials, Webinars and videos, and a user forum.The main objective of this project is to ensure ongoing maintenance for the operation of CHARMM-GUI (http://www.charmm-gui.org), a web-based graphical user interface (GUI). This will require code changes to make it a robust, sustainable web-based cyberinfrastructure that supports both expert and non-expert users from a broad range of disciplines to easily build and simulate complex biological systems. Over the past 10 years, CHARMM-GUI has proven that such a web-based GUI provides an ideal platform to build complex biological systems interactively, and prepare simulation inputs with well-established and reproducible simulation protocols. While the modules in CHARMM-GUI are all functional, similar to most academic software, they have been developed by different students and postdocs, which requires substantial code cleaning and quality control to guarantee CHARMM-GUI's sustainable operations. So, this project will (AIM 1) maintain and Improve CHARMM-GUI and (AIM 2) improve Usability. This project also seeks to foster synergistic scientific research and education by providing a well-maintained, web-based cyberinfrastructure resource to students and researchers in multiple simulation communities for any general biomolecular simulations as well as advanced modeling and simulation.

研究生物分子如何随时间弯曲或改变形状的研究人员使用非常复杂的算法作为工具，了解结构、运动和相互作用的不同方面。这些工具是更大的软件应用程序的一部分，这些应用程序捕获整个系统的行为，包括环境和生物分子中的原子和分子。随着研究人员在更长的研究间隔内，用更多的组件对更大的体积进行建模，跟踪系统中的所有元素及其属性正成为一个主要障碍，即使对经验相对丰富的计算生物学家来说也是如此。最大的挑战是在有效地执行这些复杂的模拟以解决实际问题的同时保持准确性和重复性。这个项目的目标是帮助两类研究人员：知道如何设置条件并希望保存和分享它们的专家，以及在设置所有输入方面需要指导并可能需要一些帮助来解释结果的非专家。CHARMM-图形用户界面已经解决了这些挑战，因为用户可以交互地建立复杂的生物分子系统，并很容易理解必须输入哪些文件才能进行最先进的生物分子模拟。该接口不仅限于CHARMM模拟包，尽管名为CHARMM，还包括GROMACS、Amber、Genesis、LAMMPS、Desmond、OpenMM和CHARMM/OpenMM。该项目旨在维护CHARMM-图形用户界面应用程序的独特范围，同时提高代码库的一致性，以便更容易地维护工具，并通过包含测试套件更容易地添加正确工作的新功能。该项目的总体目标是帮助学生和研究人员进行创新和新颖的生物分子建模和模拟研究，通过提供一个优秀的工具、优秀的教程文档、网络研讨会和视频以及用户论坛来获得对感兴趣的生物分子系统的结构、动力学和潜在机制的新见解。该项目的主要目标是确保CHARMM-图形用户界面(http://www.charmm-gui.org)，)的运行持续维护。这将需要修改代码，使其成为一个强大、可持续的基于网络的网络基础设施，支持来自广泛学科的专家和非专家用户轻松建立和模拟复杂的生物系统。在过去的10年里，CHARMM-图形用户界面已经证明，这样一个基于网络的图形用户界面提供了一个理想的平台，可以交互地构建复杂的生物系统，并使用完善的和可重复的模拟协议准备模拟输入。虽然CHARMM-图形用户界面中的模块都是功能性的，类似于大多数学术软件，但它们是由不同的学生和博士后开发的，这需要大量的代码清理和质量控制来保证CHARMM-图形用户界面的可持续运行。因此，这个项目将(目标1)维护和改进CHARMM-图形用户界面，(目标2)提高可用性。该项目还寻求通过向多个模拟社区的学生和研究人员提供维护良好的、基于网络的网络基础设施资源，以进行任何一般生物分子模拟以及高级建模和模拟，从而促进科学研究和教育的协同。