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相关概念视频

Muscles for Facial Expressions01:14

Muscles for Facial Expressions

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The craniofacial muscles are a collection of approximately 20 thin skeletal muscles situated beneath the skin of the face and scalp. These muscles, primarily responsible for the vast array of human facial expressions, originate from the bones or fibrous structures of the skull and extend outwards to connect with the skin. While most skeletal muscles in the body are enveloped in thick fascia, facial muscles generally have a more delicate fascial covering, with the buccinator muscle being a...
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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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Conformations of Cycloalkanes02:29

Conformations of Cycloalkanes

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Adolf von Baeyer attempted to explain the instabilities of small and large cycloalkane rings using the concept of angle strain — the strain caused by the deviation of bond angles from the ideal 109.5° tetrahedral value for sp3  hybridized carbons. However, while cyclopropane and cyclobutane are strained, as expected from their highly compressed bond angles, cyclopentane is more strained than predicted, and cyclohexane is virtually strain-free. Hence, Baeyer’s theory that...
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Assembly of Cytoskeletal Filaments01:18

Assembly of Cytoskeletal Filaments

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Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...
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Conformity01:20

Conformity

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Conformity is the change in a person’s behavior to go along with the group, even if that person does not agree with the group.
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Conformations of Butane02:20

Conformations of Butane

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Unlike ethane and propane that have only two major conformations, butane has more than two conformers. The staggered form of butane in which the bulky methyl groups on the two carbons are placed on opposite sides, that is, at a dihedral angle of 180°, is the lowest energy, most stable form — called the anti conformer. This conformation is stabilized due to the absence of steric repulsion between the largely spaced out methyl groups. The other two staggered conformations are...
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Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
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Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

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CSMILES:一个紧的,人类可读的SMILES扩展用于形状的扩展.

James W Furness1, Kevin B Moore1, Art Bochevarov1

  • 1Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, United States.

Journal of chemical information and modeling
|September 26, 2025
PubMed
概括

一个新的化学符号,Conformer-SMILES (CSMILES),编码分子3D结构和二面角在紧的字符串. 这种方法允许对分子对应物的规范表示,不变于旋转和转换,从而实现高效的数据存储和机器学习应用.

科学领域:

  • 计算化学的计算化学
  • 化学信息学 化学信息学
  • 结构生物学 结构生物学

背景情况:

  • 像SMILES这样的现有分子线符号方案缺乏区分同一分子的各种构造的能力.
  • 高效地表示和存储3D分子结构对于计算化学和药物发现至关重要.

研究的目的:

  • 开发SMILES符号的扩展,称为CSMILES,能够编码特定的分子调整器信息.
  • 为3D分子结构创建一个紧和正规的基于文本的表示,包括二面角.

主要方法:

  • CSMILES扩展了标准的SMILES,将二面角值直接纳入字符串内的键符.
  • 符合水平的规范化确保了原子重新排序,转换和旋转的不变性.
  • 在3D结构和CSMILES之间实现了一种双向转换工具,由Python代码支持.

主要成果:

  • CSMILES字符串提供了一个紧而可读的分子对应物的表示,即使是涉及分支,环和对称性的复杂结构.
  • 规范的CSMILES字符串对常见的转换是不变的,确保一致的表示.
  • 一个功能性的 Python 实现方便了在 3D 分子数据和 CSMILES 符号之间进行转换.

结论:

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  • CSMILES提供了一种新且高效的方法来表示和存储3D分子结构信息.
  • 开发的符号在开发机器学习模型中具有潜在的应用,用于依赖形状的分子性质.