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相关概念视频

Lattice Centering and Coordination Number02:33

Lattice Centering and Coordination Number

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The structure of a crystalline solid, whether a metal or not, is best described by considering its simplest repeating unit, which is referred to as its unit cell. The unit cell consists of lattice points that represent the locations of atoms or ions. The entire structure then consists of this unit cell repeating in three dimensions. The three different types of unit cells present in the cubic lattice are illustrated in Figure 1.
Types of Unit Cells
Imagine taking a large number of identical...
10.0K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.9K
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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Conserved Binding Sites01:49

Conserved Binding Sites

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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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
13.5K
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

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Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal...
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Updated: Sep 17, 2025

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

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基于格子的循环接对接的二次无约束二进制优化和约束编程方法.

J Kyle Brubaker1, Kyle E C Booth2, Akihiko Arakawa3

  • 1Amazon Advanced Solutions Lab, Seattle, WA, 98170, USA.

Scientific reports
|July 1, 2025
PubMed
概括
此摘要是机器生成的。

方位不受约束的二进制优化 (QUBO) 可以模拟-蛋白对接,但与更大的问题作斗争. 约束编程为这种结构生物学挑战提供了更具可扩展性的解决方案.

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科学领域:

  • 结构生物学 结构生物学
  • 计算生物学 计算生物学
  • 药物设计 药物设计

背景情况:

  • -蛋白相互作用对于生物过程和药物开发至关重要.
  • 对这些相互作用的准确建模对于合理的药物设计至关重要.
  • 酸蛋白对接问题带来了重大的计算挑战.

研究的目的:

  • 探索量子可调整的四进制不受约束的二进制优化 (QUBO) 对于蛋白对接的应用.
  • 在 QUBO 框架内整合循环和对接约束.
  • 为了比较一种新的QUBO方法与约束编程 (CP) 方法的性能.

主要方法:

  • 开发了一个资源高效的QUBO编码,用于-蛋白对接在四面体格子上.
  • 实施了一个端到端的框架,用于使用蛋白质数据库 (PDB) 实例评估 QUBO 和 CP 方法.
  • 在QUBO方法中使用了经典的模拟回火溶解器.
  • 开发了一种用于基准测试的新型约束编程 (CP) 方法.

主要成果:

  • QUBO方法成功地模拟了小-蛋白质对接问题 (多达6个残留物) 的可行构造.
  • 随着问题规模的增加,QUBO的性能显著下降 (例如,PDB 3WNE,5LSO).
  • 该CP方法显示出卓越的可扩展性,解决更大的实例 (多达11个残留物,PDB 2F58).

结论:

  • QUBO可以应用于-蛋白对接,但具有扩展限制.
  • 约束编程在更大的蛋白对接实例中显示出更强的性能和可扩展性.
  • 对于药物设计中复杂的蛋白对接问题,CP可能比QUBO更合适.