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
基本信息
- 批准号:10793784
- 负责人:
- 金额:$ 13.71万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 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:
- 关键词:AmberBiomedical ResearchCommunitiesComplexDevelopmentFree EnergyIon TransportLearningLigand BindingLigandsMaintenanceModelingMolecularPathologicPreparationPrevention ResearchProtocols documentationReproducibilityResearchResearch PersonnelSamplingSiteSolventsSystemTechniquesTherapeutic Agentshuman diseaseinnovationinterestmodels and simulationnovelonline resourcepreventprogramssimulationtherapeutically effective
项目摘要
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
期刊论文数量(28)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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:
- 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:
- 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:
- 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:
- 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:
- 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
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Wonpil Im的其他文献
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{{ truncateString('Wonpil Im', 18)}}的其他基金
Biophysical characterization of SARS-CoV-2 spike protein - receptor interactions
SARS-CoV-2 刺突蛋白 - 受体相互作用的生物物理特征
- 批准号:
10286279 - 财政年份:2021
- 资助金额:
$ 13.71万 - 项目类别:
Biophysical characterization of SARS-CoV-2 spike protein - receptor interactions
SARS-CoV-2 刺突蛋白 - 受体相互作用的生物物理特征
- 批准号:
10445350 - 财政年份:2021
- 资助金额:
$ 13.71万 - 项目类别:
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:
10447810 - 财政年份:2020
- 资助金额:
$ 13.71万 - 项目类别:
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:
10671554 - 财政年份:2020
- 资助金额:
$ 13.71万 - 项目类别:
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 - 财政年份:2020
- 资助金额:
$ 13.71万 - 项目类别:
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 - 财政年份:2020
- 资助金额:
$ 13.71万 - 项目类别:
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:
10027337 - 财政年份:2020
- 资助金额:
$ 13.71万 - 项目类别:
Development of Computational Toolset for Structural Systems Pharmacology
结构系统药理学计算工具集的开发
- 批准号:
9419966 - 财政年份:2018
- 资助金额:
$ 13.71万 - 项目类别:
Mechanisms & Energetics of Transmembrane-induced Signaling of Cytokine Receptors
机制
- 批准号:
8098698 - 财政年份:2010
- 资助金额:
$ 13.71万 - 项目类别:
Mechanisms & Energetics of Transmembrane-induced Signaling of Cytokine Receptors
机制
- 批准号:
7862768 - 财政年份:2010
- 资助金额:
$ 13.71万 - 项目类别:
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