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相关概念视频

Calculating Standard Free Energy Changes02:49

Calculating Standard Free Energy Changes

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The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
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Work and Energy for Variable Forces01:10

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When an object is acted upon by a variable force, the amount of work done and the change in energy of the object can be more complex to calculate compared to when a constant force is applied. Work is the product of force and displacement, while energy is the capacity of a system to do work. When a constant force is applied to an object, the work done can be calculated as the product of the force and the distance moved in the direction of the force. However, when a variable force is applied, the...
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Potential-Energy Criterion for Equilibrium01:16

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Potential energy or potential function plays an essential role in determining the stability of a mechanical system. If a system is subjected to both gravitational and elastic forces, the potential function of the system can be expressed as the algebraic sum of gravitational and elastic potential energy. If the system is in equilibrium and is displaced by a small amount, then the work done on the system equals the negative of the change in the system's potential energy from the initial to...
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Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

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Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
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The free energy change for a process may be viewed as a measure of its driving force. A negative value for ΔG represents a driving force for the process in the forward direction, while a positive value represents a driving force for the process in the reverse direction. When ΔG is zero, the forward and reverse driving forces are equal, and the process occurs in both directions at the same rate (the system is at equilibrium).
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How can we compare the energy that releases from one reaction to that of another reaction? We use a measurement of free energy to quantitate these energy transfers. Scientists call this free energy Gibbs free energy (abbreviated with the letter G) after Josiah Willard Gibbs, the scientist who developed the measurement. According to the second law of thermodynamics, all energy transfers involve losing some energy in an unusable form such as heat, resulting in entropy. Gibbs free energy...
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Updated: Jun 6, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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蛋白质工程使用可变的自由能量近似值.

Evgenii Lobzaev1,2, Michael A Herrera1, Martyna Kasprzyk1

  • 1School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.

Nature communications
|December 1, 2024
PubMed
概括
此摘要是机器生成的。

使用生成深度学习的蛋白质工程得到了PREVENT的推进,这是一个设计稳定和功能蛋白质变体的新型模型. 这种方法加速了新蛋白质的产生,成功率很高.

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科学领域:

  • 生物化学 生物化学
  • 计算生物学 计算生物学
  • 蛋白质工程是指蛋白质工程.

背景情况:

  • 蛋白质工程传统上依赖于定向进化 (DE),这是一个耗时的方法.
  • 生成型深度学习模型可以设计新的蛋白质变体,但往往缺乏热力学稳定性,产生非功能性蛋白质.

研究的目的:

  • 引入一个深度学习模型,PREVENT,用于生成热力学稳定和功能性蛋白质变体.
  • 评估PREVENT在设计大肠杆菌N-乙-L-谷氨酸激酶 (EcNAGK) 变体中的疗效.

主要方法:

  • 通过变异frEe eNergyapproximaTion (PREVENT) 开发的蛋白质工程,是一种生成的深度学习模型.
  • 在蛋白质序列和结构数据集上训练PREVENT,以学习热力学景观.
  • 应用PREVENT来设计EcNAGK酶的变体.

主要成果:

  • 预防成功地产生了40种EcNAGK的变种.
  • 85%的设计变体是功能性的.
  • 55%的功能变异表现出与野生类型酶相比的生长速度,即使有多达9个突变.

结论:

  • 与传统方法相比,PREVENT在蛋白质工程中提供了显著的加速.
  • 该模型产生稳定和功能蛋白质的能力表明了蛋白质设计的有希望的新方向.