CHARMM-GUI Development for Biomolecular Modeling and Simulation Community

生物分子建模和模拟社区的 CHARMM-GUI 开发

• 批准号: 10223386
• 负责人: Wonpil Im
• 金额: $ 33.59万
• 依托单位: LEHIGH UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10223386
• 关键词: Active Sites; Address; Amber; Biological Process; Biomedical Research; Carbohydrates; Catalysis; Communities; Complex; DNA; Development; Education; Ensure; Enzymes; Fostering; Free Energy; Gaussian model; Generations; Growth; Head; Ion Transport; Learning; Life; Ligand Binding; Ligands; Lipids; Maintenance; Methods; Modeling; Molecular; Online Systems; Outcome; Pathologic; Play; Preparation; Prevention Research; Proteins; Protocols documentation; RNA; Reader; Reproducibility; Research; Research Personnel; Resources; Role; Sampling; Site; Solvents; Standardization; Students; System; Tail; Techniques; Therapeutic Agents; Time; advanced simulation; base; cyber infrastructure; density; experience; experimental study; graphical user interface; human disease; innovation; insight; interest; models and simulation; molecular modeling; novel; online resource; prevent; programs; simulation; small molecule; theories; therapeutic development; therapeutically effective

PROJECT SUMMARY/ABSTRACT Through the development and maintenance over the past 13 years, CHARMM-GUI (http://www.charmm-gui.org) has become an essential web-based resource for the interactive construction of complex biomolecular simulation systems and the preparation of their inputs with well-established and reproducible simulation protocols for state- of-the-art molecular simulations using widely used programs, such as CHARMM, NAMD, GROMACS, AMBER, GENESIS, TINKER, LAMMPS, Desmond, and OpenMM. CHARMM-GUI has also significantly reduced the learning curve that prevents non-experts (e.g., experimentalists) from utilizing modeling and simulation to study their systems. In this application, following requests from CHARMM-GUI users and broad MD simulation package developers, three specific aims are proposed to extend the functionality of CHARMM-GUI to support a broader range of modeling and simulation community with more diverse force field selection and advanced techniques. Specifically, AIM1 is to support a more complete list of additive and polarizable force fields for all- and united-atom simulations. AIM 2 is to develop QM/MM Interfacer for QM and QM/MM calculations. Finally, AIM 3 will extend the functionality of CHARMM-GUI with non-CHARMM implicit solvent models, SILCS-based simulations (Site Identification by Ligand Competitive Saturation), ligand binding free energy calculations, constant pH simulations, replica-exchange simulations, ion transport simulations, targeted/steered simulations, and path sampling. The successful completion of the proposed project is expected to provide an effective one- stop online resource for biomedical research community to carry out innovative and novel biomolecular modeling and simulation research for the prevention and treatment of human disease.

项目概要/摘要 经过13年的开发和维护，CHARMM-GUI (http://www.charmm-gui.org) 已成为复杂生物分子模拟交互式构建的重要网络资源 系统及其输入的准备，以及状态良好且可重复的模拟协议 使用广泛使用的程序进行最先进的分子模拟，例如 CHARMM、NAMD、GROMACS、AMBER、 GENESIS、TINKER、LAMMPS、Desmond 和 OpenMM。 CHARMM-GUI 还显着减少了 防止非专家（例如实验主义者）利用建模和模拟进行研究的学习曲线 他们的系统。在此应用中，遵循 CHARMM-GUI 用户的要求和广泛的 MD 模拟 对于软件包开发人员，提出了三个具体目标来扩展 CHARMM-GUI 的功能以支持 更广泛的建模和仿真社区，具有更多样化的力场选择和先进的 技术。具体来说，AIM1 将支持更完整的可加性和极化力场列表，适用于所有- 和联合原子模拟。目标 2 是开发用于 QM 和 QM/MM 计算的 QM/MM Interfacer。最后， AIM 3 将使用基于 SILCS 的非 CHARMM 隐式溶剂模型扩展 CHARMM-GUI 的功能 模拟（通过配体竞争饱和进行位点识别），配体结合自由能计算， 恒定 pH 模拟、复制品交换模拟、离子传输模拟、定向/引导模拟、 和路径采样。拟议项目的成功完成预计将提供有效的一 停止生物医学研究界开展创新和新颖的生物分子建模的在线资源 以及人类疾病预防和治疗的模拟研究。