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: 10386324
• 负责人: Wonpil Im
• 金额: $ 11.58万
• 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/10386324
• 关键词: Amber; Biomedical Research; Communities; Complex; Development; Free Energy; Ion Transport; Learning; Ligand Binding; Ligands; Maintenance; Modeling; Molecular; Pathologic; Preparation; Prevention Research; Protocols documentation; Reproducibility; Research; Research Personnel; Sampling; Site; Solvents; System; Techniques; Therapeutic Agents; base; human disease; innovation; interest; models and simulation; novel; online resource; prevent; programs; simulation; therapeutically effective

Below is the original summary to fill this mandatory field 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.

以下是填写此必填字段的原始摘要 项目总结/摘要 CHARMM-GUI（http：//www.charmm- gui.org）已成为复杂生物分子交互构建的重要网络资源 模拟系统及其输入的准备与完善的和可再现的模拟 使用广泛使用的程序，如CHARMM，NAMD， GROMACS、AMBER、GENESIS、TINKER、LAMMPS、Desmond和OpenMM。CHARMM-GUI还 显著降低了阻止非专家（例如，实验主义者）利用 建模和仿真来研究他们的系统。在此应用程序中，根据CHARMM-GUI的请求， 用户和广泛的MD仿真软件包开发商，提出了三个具体的目标，以扩展 CHARMM-GUI的功能，以支持更广泛的建模和仿真社区， 多样的力场选择和先进的技术。具体而言，AIM 1将支持更完整的 加性和极化力场的所有和联合原子模拟。目标2是开发QM/MM接口 用于QM和QM/MM计算。最后，AIM 3将扩展CHARMM-GUI的功能， CHARMM隐式溶剂模型，基于SILCS的模拟（通过配体竞争性 饱和），配体结合自由能计算，恒定pH模拟，复制交换模拟， 离子传输模拟、目标/操纵模拟和路径采样。圆满完成 拟议的项目有望为生物医学研究提供有效的一站式在线资源 社区开展创新和新颖的生物分子建模和模拟研究，以预防 治疗人类疾病。