Search research articles

关于 JoVE

概览领导团队博客 JoVE 帮助中心

作者

出版流程编辑委员会范围与政策同行评审常见问题投稿

图书馆员

用户评价订阅访问资源图书馆顾问委员会常见问题

研究

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments 存档

教育

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual 教师资源中心教师网站

使用条款与条件

相关概念视频

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

您也可能阅读

相关文章

通过共同作者、期刊和引用图与本文相关的文章。

排序

Same author

Solving Constrained Optimization Problems Using Hybrid Qubit-Qumode Quantum Devices.

Journal of chemical theory and computation·2026

Same author

Crystal structure and molecular dynamics simulations of rademikibart Fab-IL-4Rα complex reveal biochemical basis for next-generation potent IL-4Rα inhibition in type 2 allergic and inflammatory diseases.

bioRxiv : the preprint server for biology·2026

Same author

Advancing Reproducibility and Open Data in Theoretical and Computational Chemistry.

Journal of chemical theory and computation·2026

Same author

Insights on Covalent Attachment of a Re Bipyridyl Catalyst onto <i>p</i>-Si(111) Using an Alkyl Linker for Photoelectrochemical CO<sub>2</sub> Reduction.

Inorganic chemistry·2026

Same author

Electrochemical Nitrate Reduction to Ammonia Driven by Catalytic Monovacancies in Single-Walled Carbon Nanotubes.

The journal of physical chemistry letters·2026

Same author

Mechanism of Tyrosine-Driven Deprotonation in Photosystem II Revealed by Multiscale Simulations.

Journal of the American Chemical Society·2026

Search research articles

相关实验视频

Updated: Jul 28, 2025

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

MDiGest:一个Python包,用于从分子动力学模拟中描述.

Federica Maschietto¹, Brandon Allen¹, Gregory W Kyro¹

¹Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA.

The Journal of chemical physics

|June 5, 2023

概括

本研究介绍了MDiGest,这是一个Python包,用于使用分子动力学模拟来分析蛋白质. 它揭示了蛋白质内部复杂的通信通路,有助于设计新疗法.

科学领域:

生物化学和结构生物学
计算生物学和生物信息学

背景情况:

体调节对生物过程至关重要,涉及远处蛋白位点之间的通信.
了解全性通路是阐明生化机制和工程蛋白质功能的关键.
当前的方法通常依赖于有限的原子描述器来分析蛋白质通信网络.

研究的目的:

为了介绍MDiGest,一个新的Python软件包,用于全面的全精卵研究.
通过分子动力学模拟来分析蛋白质动力学和通信通路.
提供先进的工具来比较与allostery相关的网络结构和社区动态.

主要方法:

使用生物化学系统的分子动力学 (MD) 模拟.
采用网络理论来分析分子描述符的对对相关性.
包括多种方法:原子位移相关性,二面角相关性和卡布希-桑德静电合相关性.
包括主要组件分析 (PCA) 和根平均平方波动 (RMSF) 等补充工具.

主要成果:

MDiGest提供了一个多功能工具包,用于描述超出单个原子描述器的蛋白质动态.
该软件有助于比较全性网络和社区结构.
提供了有关全性机制的物理信息的见解.

更多相关视频

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

相关实验视频

Last Updated: Jul 28, 2025

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

结论:

MDiGest增强了对蛋白质中的全沟通的研究.
该软件包支持蛋白质的工程和针对性全调节器的开发.
它提供了一个强大的平台,深入分析蛋白质动力学和全性通路.