Direct Molecular Conformation Generation

• URL: http://arxiv.org/abs/2202.01356v1
• Date: Thu, 3 Feb 2022 01:01:58 GMT
• Title: Direct Molecular Conformation Generation
• Authors: Jinhua Zhu, Yingce Xia, Chang Liu, Lijun Wu, Shufang Xie, Tong Wang, Yusong Wang, Wengang Zhou, Tao Qin, Houqiang Li, Tie-Yan Liu
• Abstract summary: We propose a method that directly predicts the coordinates of atoms. Our method achieves state-of-the-art results on four public benchmarks.
• Score: 217.4815525740703
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: 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 distance-based methods first predict interatomic distances and then generate conformations based on them, which could result in conflicting distances. In this work, we propose a method that directly predicts the coordinates of atoms. We design a dedicated loss function for conformation generation, which is invariant to roto-translation of coordinates of conformations and permutation of symmetric atoms in molecules. We further design a backbone model that stacks multiple blocks, where each block refines the conformation generated by its preceding block. Our method achieves state-of-the-art results on four public benchmarks: on small-scale GEOM-QM9 and GEOM-Drugs which have $200$K training data, we can improve the previous best matching score by $3.5\%$ and $28.9\%$; on large-scale GEOM-QM9 and GEOM-Drugs which have millions of training data, those two improvements are $47.1\%$ and $36.3\%$. This shows the effectiveness of our method and the great potential of the direct approach. Our code is released at \url{https://github.com/DirectMolecularConfGen/DMCG}.

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