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: 10793784
• 负责人: Wonpil Im
• 金额: $ 13.71万
• 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/10793784
• 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; 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 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 经过13年的发展和维护，CHARMM-GUI已经成为一个 复杂生物分子模拟系统交互式构建的基本网络资源 和准备他们的输入与完善的和可重复的模拟协议的状态- 使用广泛使用的程序，如CHARMM，NAMD，GROMACS， AMBER、GENESIS、TINKER、LAMMPS、Desmond和OpenMM。CHARMM-GUI还显著地 减少了防止非专家（例如，实验者）利用建模 和模拟来研究他们的系统。在此应用程序中，CHARMM-GUI用户的以下请求 和广泛的MD模拟包开发人员，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。

项目成果

Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane

• DOI: 10.1021/acs.jpcb.0c04553
• 发表时间: 2020-08-20
• 期刊: JOURNAL OF PHYSICAL CHEMISTRY B
• 影响因子: 3.3
• 作者: Woo, Hyeonuk;Park, Sang Jun;Im, Wonpil
• 通讯作者: Im, Wonpil

TRPV4-Rho GTPase complex structures reveal mechanisms of gating and disease.

• DOI: 10.1038/s41467-023-39345-0
• 发表时间: 2023-06-23
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Kwon, Do Hoon;Zhang, Feng;McCray, Brett A. A.;Feng, Shasha;Kumar, Meha;Sullivan, Jeremy M. M.;Im, Wonpil;Sumner, Charlotte J. J.;Lee, Seok-Yong
• 通讯作者: Lee, Seok-Yong

Practical Guidance for Consensus Scoring and Force Field Selection in Protein-Ligand Binding Free Energy Simulations.

蛋白质-配体结合自由能模拟中共识评分和力场选择的实用指南。

• DOI: 10.1021/acs.jcim.2c01115
• 发表时间: 2022
• 期刊: Journal of chemical information and modeling
• 影响因子: 5.6
• 作者: Zhang,Han;Kim,Seonghoon;Im,Wonpil
• 通讯作者: Im,Wonpil

CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides.

• DOI: 10.1021/acs.jcim.0c01360
• 发表时间: 2021-02-22
• 期刊: Journal of chemical information and modeling
• 影响因子: 5.6
• 作者: Gao Y;Lee J;Smith IPS;Lee H;Kim S;Qi Y;Klauda JB;Widmalm G;Khalid S;Im W
• 通讯作者: Im W

Additive CHARMM36 Force Field for Nonstandard Amino Acids.

• DOI: 10.1021/acs.jctc.1c00254
• 发表时间: 2021-06-08
• 期刊: Journal of chemical theory and computation
• 影响因子: 5.5
• 作者: Croitoru A;Park SJ;Kumar A;Lee J;Im W;MacKerell AD Jr;Aleksandrov A
• 通讯作者: Aleksandrov A