使用CONFORGE生成高质量的符合器:算法和性能评估
Thomas Seidel1, Christian Permann2, Oliver Wieder3
1Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
Journal of chemical information and modeling
|August 25, 2023
概括
一个新的开源工具CONFORGE可以为药物设计生成精确的分子构造. 它的性能优于其他开源选项,并与小型分子的商业软件相匹配,在宏观循环的准确性方面表现出色.
科学领域:
- 计算化学是一种计算化学.
- 分子建模分子建模
- 药物发现 药物发现
背景情况:
- 精确的分子构造对于计算机辅助药物设计 (CADD) 至关重要.
- 现有的开源适配器发电机往往落后于商业替代品.
- 为了预测分子结合,需要有效地生成具有代表性的符合组合.
研究的目的:
- 介绍CONFORGE,一个开源的符合组合生成器.
- 在准确性和效率方面,将CONFORGE与商业和开源工具进行比较.
- 评估药物样小分子和宏循环结构的性能.
主要方法:
- 使用CONFORGE.使用Conformer组合生成.
- 与已建立的商业和开源软件进行比较.
- 在复制实验3D结构时的准确性评估.
- 计算效率和稳健性的评估.
主要成果:
- 在用于小分子的开源工具中,CONFORGE 展示了卓越的性能.
- 在速度和准确性方面,CONFORGE与小型分子商业软件的性能相匹配或超越.
- 对于宏观循环,CONFORGE在基准研究中实现了最高的平均准确性.
结论:
- CONFORGE 提供了最先进的性能,用于生成分子适配器.
- 它为药物设计提供了一个强大,准确和高效的开源替代方案.
- CONFORGE对于生成宏环化合物的精确构造特别有效.
相关概念视频
Conformity
45.2K
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.
45.2K
Conformations of Cycloalkanes
11.9K
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...
11.9K
Compacting Factor test
187
The compacting factor test is a method used to assess the workability of concrete. It is especially suitable for concrete mixes containing aggregates up to one and a half inches in size. This test involves specialized equipment consisting of two truncated cone-shaped hoppers and a cylinder, all with polished interior surfaces to minimize friction.
The procedure begins by placing concrete into the upper hopper without any compaction. Once filled, the bottom door of this hopper is opened,...
The procedure begins by placing concrete into the upper hopper without any compaction. Once filled, the bottom door of this hopper is opened,...
187
Protein Folding Quality Check in the RER
3.7K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
3.7K
Conformations of Cyclohexane
12.6K
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...
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...
12.6K
Conformations of Ethane and Propane
14.1K
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...
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...
14.1K


