论文标题
直接分子构象产生
Direct Molecular Conformation Generation
论文作者
论文摘要
分子构象的产生旨在产生分子中所有原子的三维坐标，并且是生物信息学和药理学中的重要任务。以前的方法通常首先预测原子间距离，原子间距离的梯度或分子的局部结构（例如扭转角），然后重建其3D构象。没有完全探索无上述中间值的直接生成构象。在这项工作中，我们提出了一种直接预测原子坐标的方法：（1）损耗函数对于坐标的旋转旋转和对称原子的允许而不变； （2）新提出的模型适应键合键和原子信息，并迭代地完善了生成构象的坐标。我们的方法在GEOM-QM9和GEOM-DRUGS数据集上取得了最佳结果。进一步的分析表明，我们生成的构象具有具有地面构象的更接近性能（例如，同性恋间隙）。此外，我们的方法通过提供更好的初始构象来改善分子对接。所有结果都证明了我们方法的有效性以及直接方法的巨大潜力。该代码在https://github.com/directmolecularconfgen/dmcg上发布
Molecular conformation generation aims to generate three-dimensional coordinates of all the atoms in a molecule and is an important task in bioinformatics and pharmacology. Previous methods usually first predict the interatomic distances, the gradients of interatomic distances or the local structures (e.g., torsion angles) of a molecule, and then reconstruct its 3D conformation. How to directly generate the conformation without the above intermediate values is not fully explored. In this work, we propose a method that directly predicts the coordinates of atoms: (1) the loss function is invariant to roto-translation of coordinates and permutation of symmetric atoms; (2) the newly proposed model adaptively aggregates the bond and atom information and iteratively refines the coordinates of the generated conformation. Our method achieves the best results on GEOM-QM9 and GEOM-Drugs datasets. Further analysis shows that our generated conformations have closer properties (e.g., HOMO-LUMO gap) with the groundtruth conformations. In addition, our method improves molecular docking by providing better initial conformations. All the results demonstrate the effectiveness of our method and the great potential of the direct approach. The code is released at https://github.com/DirectMolecularConfGen/DMCG
