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相关概念视频

Newman Projections02:06

Newman Projections

16.8K
Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...
16.8K
Conformations of Ethane and Propane02:18

Conformations of Ethane and Propane

13.9K
In an organic molecule, free rotation about the carbon-carbon single bond results in energetically different conformers of the molecule. Due to this rotation, called the internal rotation, ethane has two major conformations — staggered and eclipsed.
Staggered conformation is a low energy and more stable conformation with the C-H bonds on the front carbon placed at 60°dihedral angles relative to the C-H bonds on the back carbon, leading to a reduced torsional strain. In staggered...
13.9K
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

34.3K
VSEPR Theory for Determination of Electron Pair Geometries
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Conformations of Cyclohexane02:11

Conformations of Cyclohexane

12.4K
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 Butane02:20

Conformations of Butane

14.2K
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...
14.2K
Conformations of Cycloalkanes02:29

Conformations of Cycloalkanes

11.8K
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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使用内部坐标和生成方向图形卷积神经网络有效生成符合组合.

Eugene Raush1, Ruben Abagyan2, Maxim Totrov1

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概括

我们开发了GINGER,这是一个神经网络算法,用于快速生成分子适应器. 这种方法有效地从二维化学图表中预测低能量的3D分子结构,加速药物发现.

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科学领域:

  • 计算化学的计算化学
  • 化学中的人工智能.
  • 分子建模分子建模

背景情况:

  • 准确预测分子3D结构对于理解化学和生物过程至关重要.
  • 传统的适应器生成方法在计算上可能是昂贵和缓慢的,这限制了它们对大数据集的应用.
  • 开发高吞吐量和精确的算法用于分子调整器生成是计算化学的一个持续挑战.

研究的目的:

  • 介绍一种基于神经网络的新算法,用于高通量分子适应器生成.
  • 通过使用内部坐标表示,从二维化学拓中预测低能变态.
  • 提供一种计算效率高,准确的方法来生成符合组合.

主要方法:

  • 一个化学图形-卷积网络被训练来预测使用内部坐标 (键长,键和扭转角度) 的低能变态.
  • 一个生成的神经网络架构被用于扭力空间中的denoising,生成与扭力能量配置文件相关的符合组合.
  • 基于力场的能量最小化被用来改进生成的对应器,并对计算密集的阶段进行GPU优化.

主要成果:

  • 在标准 PDB 测试集上进行基准测试时,GINGER 算法在符合性回收方面表现出高度竞争力的结果.
  • 该方法实现了高吞吐率,适合处理大规模的复合库 (千兆级).
  • 由GINGER生成的调节器组合显示,种群与扭力能量概况有很好的相关性.

结论:

  • GINGER算法提供了一种高效和准确的方法,用于高通量分子适应器生成.
  • 这种方法显著提高了处理大型化学库的能力,用于药物发现和分子建模.
  • 有一个用于交互式调节器生成和查看的Web服务器,可方便更广泛的访问和应用.