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Updated: Jun 11, 2025

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

Published on: July 14, 2015

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鱼使进化同类和功能类型在不可分离和无序序列中的敏感检测成为可能

Chi Fung Willis Chow1,2,3, Soumyadeep Ghosh1,2, Anna Hadarovich1,2

  • 1Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.

Proceedings of the National Academy of Sciences of the United States of America
|October 9, 2024
PubMed
概括

我们开发了SHARK-dive,这是一种无对齐的工具,用于识别内在无序区域 (IDR) 的同质性. 这种方法准确地检测出功能上相似的IDR,克服了快速进化序列的传统对齐式方法的局限性.

关键词:
同质性检测 检测 同质性检测本质上是无序的蛋白质区域.机器学习是机器学习.序列到函数范式范式的顺序

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An Integrated Approach for Microprotein Identification and Sequence Analysis09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

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Evolutionary Relationships through Genome Comparisons02:54

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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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.
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Evolution shapes the features of organisms over time, ensuring that they are suited for the environments in which they live. Sometimes, selection pressure leads to the rise of similar but unrelated adaptations in organisms with no recent common ancestors, a process known as convergent evolution.
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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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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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