Center for Macromolecular Modeling and Bioinformatics

项目摘要/摘要 大分子建模和生物信息学生物医学技术研究资源，以下简称 简单地说就是“中心”，开发了软件工具来模拟原子和粗略的细胞过程- 粒度级。该中心经验丰富的多学科研究团队为生物医学提供 研究界使用“计算显微镜”，并与领先的实验实验室合作。这个 配备分子可视化、序列、结构和动力学分析的计算显微镜 功能，目前由NAMD、VMD和晶格微生物软件程序组成，这些程序是免费和开放的- 消息来源。该中心将把其计算工具的使用扩展到广泛的生物医学研究问题 并为生物医学研究社区提供轻松获取这些工具的途径。在下一个资助期， 中心将追求以下目标： ·提高长时间、大长度的细胞过程模拟的性能、ffi准确性和准确性 鳞片； ·通过提供可访问的模拟工具支持，促进生物医学研究领域的创新- 尤其是先进的多拷贝增强采样协议、QM/MM、多分辨率方法 粗粒度模型、生化反应大型网络的随机模拟、布朗动力学、 和全细胞模拟； ·将最先进的GPU、千兆级和百亿级计算技术的实施带入 分子和细胞层面的生物医学研究； ·通过功能强大、可定制的软件包支持生物分子系统的可视化和分析， 集成多模式实验成像(例如，低温电子显微镜和层析成像、X射线、核磁共振) 和-组学数据以及建模和模拟工具； ·增强大尺寸和长时间尺度细胞PRO的可视化、分析和建模性能 通过利用新兴技术(如GPU加速、远程可视化和非易失性 记忆； ·开发对整个细胞行为和膜环境等大型细胞组件建模的方法 和染色质； ·将粗粒度模拟方法扩展到真核大小的细胞； ·通过与两个理论部门的合作，推动新计算工具和方法的开发 和实验实验室； ·利用电子教科书和视频加强服务、培训和传播，提供 尖端计算实验室、云计算资源、实践培训、fi一流教育 材料，以及一个广泛使用的生物医学研究人员网站。

Project Summary / Abstract The Biomedical Technology Research Resource for Macromolecular Modeling and Bioinformatics, hereafter referred to simply as the “Center,” develops software tools to model cellular processes at both the atomic and coarse- grained level. An experienced, multidisciplinary team of researchers at the Center provides for the biomedical research community a “computational microscope” and collaborates with leading experimental laboratories. The computational microscope, equipped with molecular visualization, sequence, structure and dynamics analysis capabilities, presently consists of NAMD, VMD, and Lattice Microbes software programs that are free and open- source. The Center will expand the use of its computational tools to a broad range of biomedical research problems and provide easy access to these tools for the biomedical research community. In the next funding period, the Center will pursue the following goals: · Raise performance, efficiency, and accuracy of simulations for cellular processes at long time and large length scales; · Facilitate innovation in the biomedical research community by providing accessible simulation tools support- ing, in particular, advanced multi-copy enhanced sampling protocols, QM/MM, multi-resolution methods, coarse-grained models, stochastic simulations of large networks of biochemical reactions, Brownian dynamics, and whole cell simulations; · Lead the implementation of state of the art technologies in GPU, petascale, and pre-exascale computing into biomedical research at the molecular and cellular level; · Support visualization and analysis of biomolecular systems with powerful, customizable software packages, integrating multi-modal experimental imaging (e.g., cryo-electron microscopy and tomography, X-ray, NMR) and -omics data with model building and simulation tools; · Enhance performance for visualization, analysis, and modeling of large-size and long-timescale cellular pro- cesses by exploiting emerging technologies such as GPU acceleration, remote visualization, and non-volatile memory; · Develop methods to model whole cell behavior and large cellular components such as membrane environments and chromatin; · Scale coarse-grained simulation methods to eukaryotic-sized cells; · Drive the development of novel computational tools and methods through collaborations with both theoretical and experimental laboratories; · Enhance service, training, and dissemination with the use of electronic text books and videos, providing a cutting edge computational laboratory, cloud computing resources, hands-on training, first-rate educational material, and an extensive, widely-used website to biomedical researchers.