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相关概念视频

Improving Translational Accuracy02:07

Improving Translational Accuracy

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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
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Per-Unit Sequence Models01:26

Per-Unit Sequence Models

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An ideal Y-Y transformer, grounded through neutral impedances, displays per-unit sequence networks akin to those of a single-phase ideal transformer when subjected to balanced positive- or negative-sequence currents. These currents do not produce neutral currents, and their associated voltage drops.
Zero-sequence currents, which are identical in magnitude and phase, generate a neutral current, resulting in voltage drops across the neutral impedance and the low-voltage winding. If the...
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Protein Complex Assembly02:41

Protein Complex Assembly

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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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相关实验视频

Updated: Jul 15, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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集成无监督语言模型与多视图多序列对齐,以实现高精度的链间接触预测.

Zi Liu1, Yi-Heng Zhu2, Long-Chen Shen3

  • 1School of Computer Science and Engineering, Nanjing University of Science and Technology, Xiaolingwei 200, Nanjing, 210094, China; Computer Department, Jingdezhen Ceramic University, Jingdezhen, 333403 , China.

Computers in biology and medicine
|September 25, 2023
PubMed
概括

ICCPred是一种新的深度学习方法,使用氨基酸序列准确预测蛋白质链间接触. 这种方法提高了对蛋白质复杂结构和功能的理解.

关键词:
共同进化的多样性多样性深度残留网络深度残留网络连锁链间接触预测多个序列对齐的调整.预先训练有素的语言模型

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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A Practical Guide to Phylogenetics for Nonexperts
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A Practical Guide to Phylogenetics for Nonexperts

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相关实验视频

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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科学领域:

  • 计算生物学 计算生物学
  • 结构生物学 结构生物学
  • 生物信息学是一种生物信息学.

背景情况:

  • 准确识别链间接触对于确定蛋白质复杂的3D结构和生物功能至关重要.
  • 从氨基酸序列中预测链间接触的现有方法有局限性.

研究的目的:

  • 开发一种新的深度学习方法,ICCPred,仅使用氨基酸序列来准确预测蛋白质复合体中的链际接触.
  • 与最先进的方法相比,提高链间接触预测的准确性.

主要方法:

  • 开发了ICCPred,这是一个使用深度残余网络架构的深度学习管道.
  • 集成了一个预先训练的语言模型,其中包含来自不同生物视角的三个多重序列对齐 (MSA).
  • 在709个非冗余蛋白质复合体上训练和评估模型.

主要成果:

  • ICCPred显著提高了链间接触预测的准确性.
  • 该方法的性能优于现有的最先进的方法.
  • 分析显示,预训练的变压器语言模型有效地捕捉了来自MSA的共同进化多样性,提高了预测准确度.

结论:

  • ICCPred提供一种基于深度学习的高度准确的方法,仅从蛋白质序列预测链际接触.
  • 该方法为大规模的蛋白质-蛋白质相互作用注释和结构生物学研究提供了有价值的工具.