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相关概念视频

Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

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Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...
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Catalytically Perfect Enzymes01:07

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The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
 
Most enzymes...
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Introduction to Enzyme Kinetics01:19

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Enzyme kinetics studies the rates of biochemical reactions. Scientists monitor the reaction rates for a particular enzymatic reaction at various substrate concentrations. Additional trials with inhibitors or other molecules that affect the reaction rate may also be performed.
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...
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Enzyme Kinetics01:19

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Enzymes speed up reactions by lowering the activation energy of the reactants. The speed at which the enzyme turns reactants into products is called the rate of reaction. Several factors impact the rate of reaction, including the number of available reactants. Enzyme kinetics is the study of how an enzyme changes the rate of a reaction.
Scientists typically study enzyme kinetics with a fixed amount of enzyme in the controlled environment of a test tube. When more reactant, or substrate, is...
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Introduction to Enzymes01:22

Introduction to Enzymes

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The use of enzymes by humans dates to 7000 BCE. Humans first used enzymes to ferment sugars and produce alcohol without knowing that this was an enzyme-catalyzed reaction. Wilhelm Kuhne coined the term 'enzyme' in 1877 from the Greek words ‘en’ meaning ‘in’ or ‘within’ and ‘zyme’ meaning ‘yeast.’
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Enzymes02:34

Enzymes

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Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
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A Protocol for Computer-Based Protein Structure and Function Prediction
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使用可解释的优化合体学习框架预测酶功能.

Saikat Dhibar1, Sumon Basak1, Biman Jana1

  • 1School of Chemical Sciences, Indian Association for the Cultivation of Science Jadavpur Kolkata-700032 India pcbj@iacs.res.in.

Chemical science
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概括
此摘要是机器生成的。

我们开发了SOLVE,这是一种可解释的机器学习方法,用于仅使用蛋白质序列来预测酶功能. SOLVE提高了准确性,并确定了关键的功能动机,帮助生物研究和药物设计.

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科学领域:

  • 生物信息学是一种生物信息学.
  • 计算生物学 计算生物学
  • 酶催化酶的催化作用

背景情况:

  • 准确的酶功能预测对于生物研究至关重要,特别是对于新型序列.
  • 现有的机器学习工具在特征提取,可解释性和概括性方面面临挑战.

研究的目的:

  • 开发一种可解释的机器学习方法,用于准确的酶功能预测.
  • 解决当前ML工具在特征提取和解释性方面的局限性.

主要方法:

  • 构建了一个专门的酶功能数据集.
  • 开发了SOLVE (Soft-Voting Optimized Learning for Versatile Enzymes),一个使用随机森林,LightGBM和决策树的整体ML模型.
  • 从主要蛋白质序列和沙普利分析中采用了代币化的次序来解释可解释性.

主要成果:

  • SOLVE实现了高预测准确度,区分了酶与非酶,并分配了酶委员会 (EC) 号码.
  • 该方法有效地通过使用焦点损失惩罚来缓解类不平衡.
  • 在催化和全位点确定了功能性动图,提高了可解释性.

结论:

  • SOLVE提供了一种精简,准确和可解释的方法,用于仅使用初级序列数据进行高通量酶功能的预测.
  • 在独立数据集上优于现有的工具,对生物研究和治疗药物设计有希望.