Collaborative: SI2-SSE - A Plug-and-Play Software Platform of Robotics-Inspired Algorithms for Modeling Biomolecular Structures and Motions

协作：SI2-SSE - 用于生物分子结构和运动建模的机器人启发算法的即插即用软件平台

• 批准号: 1440523
• 负责人: Adrian Roitberg
• 金额: $ 6.72万
• 依托单位: University of Florida
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-02-01 至 2018-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1440523&HistoricalAwards=false
• 关键词: Collaborative; SI2; SSE; Plug; Play

This project aims to develop a novel plug-and-play platform of open-source software elements to advance algorithmic research in molecular biology. The focus is on addressing the algorithmic impasse faced by computational chemists and biophysicists in structure-function related problems involving dynamic biomolecules central to our biology. The software platform resulting from this project provides the critical software infrastructure to support transformative research in molecular biology and computer science that benefits society at large by advancing our modeling capabilities and in turn our understanding of the role of biomolecules in critical mechanisms in a living and diseased cell.The project addresses the current impasse on the length and time scales that can be afforded in biomolecular modeling and simulation. It does so by integrating cutting-edge knowledge from two different research communities, computational chemists and biophysicists focused on detailed physics-based simulations, and AI researchers focused on efficient search and optimization algorithms. The software elements integrate sophisticated energetic models and molecular representations with powerful search and optimization algorithms for complex modular systems inspired from robot motion planning. The plug-and-play feature of the software platform supports putting together novel algorithms, such as wrapping Molecular Dynamics or Monte Carlo as local search operators within larger robotics-inspired exploration frameworks, and adding emerging biomolecular representations, models, and search techniques even beyond the timeline of this project.

该项目旨在开发一个新的开源软件元素即插即用平台，以推进分子生物学的算法研究。重点是解决计算化学家和生物化学家在结构-功能相关问题中所面临的算法僵局，这些问题涉及到我们生物学中的动态生物分子。该项目产生的软件平台提供了关键的软件基础设施，以支持分子生物学和计算机科学的变革性研究，通过提高我们的建模能力，进而提高我们对生物分子在活细胞和病变细胞中关键机制中的作用的理解，造福于整个社会。该项目解决了目前生物分子建模中可以提供的长度和时间尺度的僵局和仿真它通过整合来自两个不同研究社区的前沿知识来实现这一目标，计算化学家和生物化学家专注于详细的基于物理的模拟，人工智能研究人员专注于高效的搜索和优化算法。软件元素将复杂的能量模型和分子表示与强大的搜索和优化算法集成在一起，这些算法适用于受机器人运动规划启发的复杂模块化系统。该软件平台的即插即用功能支持将新算法组合在一起，例如将分子动力学或蒙特卡罗作为本地搜索算子包装在更大的机器人启发的探索框架中，并添加新兴的生物分子表示，模型和搜索技术，甚至超出了该项目的时间轴。