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相关概念视频

Per-Unit Sequence Models01:26

Per-Unit Sequence Models

409
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...
409
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 and Protein Structure02:15

Protein and Protein Structure

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
86.6K
Improving Translational Accuracy02:07

Improving Translational Accuracy

14.0K
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...
14.0K
Improving Translational Accuracy02:07

Improving Translational Accuracy

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Conservation of Protein Domains02:26

Conservation of Protein Domains

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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预训练的蛋白质语言模型在序列新性和结构完整性之间进行选择.

Arjuna M Subramanian1, Zachary A Martinez1, Matt Thomson1

  • 1Division of Biology and Biological Engineering, California Institute of Technology, CA, USA.

bioRxiv : the preprint server for biology
|November 19, 2025
PubMed
概括

蛋白质语言模型 (PLM) 可以产生新的序列,但与结构多样性作斗争,经常陷入"螺旋捆陷". 需要新的策略来引导PLM产生多样化,生物物理上有效的蛋白质设计.

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.
  • 生物化学中的人工智能

背景情况:

  • 蛋白质语言模型 (PLM) 越来越多地用于蛋白质设计和变异效应预测.
  • 了解生物物理规则和自然蛋白质空间的多样性对于推进PLM能力至关重要.

研究的目的:

  • 以计算方式描述和描述PLM生成的小蛋白质的序列和结构统计.
  • 评估PLM输出对自然蛋白质多样性和生物物理规则的总结程度.

主要方法:

  • 免费,不受约束的几十万个小蛋白质的生成使用建筑上不同的PLM.
  • 序列和结构统计和属性的计算分析.

主要成果:

  • PLM显示出产生新型氨基酸序列的高能力.
  • 与天然蛋白质相比,PLM生成的蛋白质具有有限的结构变异.
  • 在序列新性和结构宽度之间存在权衡,在自然序列空间之外倾向于"螺旋捆陷".

结论:

  • PLM可以产生新的序列,但难以复制自然蛋白质的结构多样性.
  • 当前的PLM设计策略可能受到特定结构动机的趋势的限制.

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  • 开发新方法对于引导PLM产生更广泛的生物物理有效蛋白质结构和功能至关重要.