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相关概念视频

Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
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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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Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
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Factors Affecting Dissolution: Polymorphism, Amorphism and Pseudopolymorphism01:21

Factors Affecting Dissolution: Polymorphism, Amorphism and Pseudopolymorphism

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Polymorphism refers to the existence of a drug substance in multiple crystalline forms, known as polymorphs. Recently, this term has been expanded to include solvates (forms containing a solvent), amorphous forms (non-crystalline forms), and desolvated solvates (forms from which the solvent has been removed).
Some polymorphic crystals possess lower aqueous solubility than their amorphous counterparts, leading to incomplete absorption. For instance, the oral suspension of Chloramphenicol, which...
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Protein Folding01:22

Protein Folding

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Overview
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Variability: Analysis01:11

Variability: Analysis

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Measures of variability are statistical metrics that reveal the dispersion pattern within a dataset. They are pivotal in biostatistics, providing insights into the heterogeneity within health and biological data. Variability signifies the degree to which data points diverge from one another, helping researchers understand the potential range of values and associated uncertainty within the data.
The range is a simple measure of variability, indicating the difference between the highest and...
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A Protocol for Computer-Based Protein Structure and Function Prediction
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酶结构与变异效应可预测性相关.

Floris van der Flier1, Dave Estell2, Sina Pricelius3

  • 1Department of Plant Sciences, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands.

Computational and structural biotechnology journal
|October 22, 2024
PubMed
概括
此摘要是机器生成的。

用于蛋白质工程的机器学习模型显示了可变的准确性. 结构特征,如埋藏和活动地点的近距离显著影响预测错误,建议改进变异效应预测 (VEP) 模型.

关键词:
机器学习是机器学习.可以预测的可预测性.蛋白质工程是一种蛋白质工程.

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科学领域:

  • 计算生物学是一种计算生物学.
  • 蛋白质工程是一种蛋白质工程.
  • 机器学习是机器学习.

背景情况:

  • 机器学习模型越来越多地用于预先选蛋白质变体.
  • 目前的模型显示不同蛋白质变体的可变预测准确性.
  • 具有较大的预测误差的变体的特征尚未得到充分理解.

研究的目的:

  • 调查结构特征是否影响蛋白质变异效应的可预测性.
  • 识别机器学习模型中与预测错误相关的特定结构特征.
  • 引导机器学习引导蛋白质工程的改进.

主要方法:

  • 创建了3,706种酶变体的高阶组合数据集.
  • 根据结构特征 (埋葬,接触残留物,活动地点的近距离,次要结构) 分区了数据集.
  • 在这些分区子集上训练并评估了四种监督变异效应预测 (VEP) 模型.

主要成果:

  • 可预测性在很大程度上取决于所有四个测试的结构特征.
  • 这些依赖关系在所有四个测试的VEP模型中都是一致的.
  • 这些发现表明,当前的算法并不完全考虑结构-功能决定因素.

结论:

  • 结构特征显著影响蛋白质变异效应的可预测性.
  • 通过结合新的诱导偏差和数据模式,可以实现VEP模型的改进.
  • 分层数据集设计对于识别机器学习引导的蛋白质工程改进领域至关重要.