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MolEM:用于分子图和序列顺序的统一生成框架
Hanwen Zhang1,2, Deng Xiong3, Xianggen Liu1,2
1College of Computer Science, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China.
Briefings in bioinformatics
|March 31, 2025
概括
摩尔EM共同学习3D分子图和它们的序列顺序,改进药物设计. 这种新的框架产生具有高结合亲和度和现实的结构的分子,优于现有的方法.
科学领域:
- 计算化学是一种计算化学.
- 药物发现 药物发现
- 机器学习 机器学习
背景情况:
- 基于结构的药物设计旨在为蛋白质标创建高亲和度分子.
- 当前的顺序生成模型与分子图表排序的计算难以处理性作斗争.
- 现有的方法使用固定的订单方案,导致由于松散的概率界限导致低于最佳的生成.
研究的目的:
- 开发一个统一的生成框架,用于共同学习3D分子图及其序列顺序.
- 解决分子图表生成中固定的订单方案的局限性.
- 在药物设计中提高连接体形状的准确性和灵活性.
主要方法:
- 提出了MolEM,这是一个统一的生成框架,用于联合3D分子图和顺序序的学习.
- 通过使用变量期望-最大化算法,推导和最大化了可能性的紧密下界.
- 集成的QuickVina 2用于分子对接,以优化结合姿势和连接体构造.
主要成果:
- 在产生具有高结合亲和度的分子方面,MolEM显著优于基线模型.
- 该框架产生具有现实的结构的分子.
- MolEM高效地近似真边缘图形概率,并识别出化学相关的顺序.
结论:
- 摩尔EM为基于学习的订单方案提供了一种新的方法,用于3D分子图形生成.
- 对图形和顺序的联合学习提高了分子生成质量.
- 这种方法通过允许更准确和更灵活的连接体形状来推进基于结构的药物设计.
相关概念视频
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The Frost circle or the inscribed polygon method is a graphical method for determining the relative energies of π molecular orbitals (MOs) for planar, fully conjugated, and monocyclic compounds. This method was first described by A. A. Frost and Boris Musulin in 1953.
A Frost circle is constructed by drawing a polygon whose number of edges is equal to the number of carbons of the given cyclic system, with one of the vertices pointing down. Then, a circle is drawn enclosing the polygon so that...
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