# Equivalent Distance Geometry Error for Molecular Conformation Comparison

arXiv: https://arxiv.org/abs/2201.08714 · HTML: https://mlsanity.com/paper/2201.08714/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 8 of its 13 references that are in the map.
- First posted on arXiv 13 Nov 2021.

## Builds on (most cited first, 8 of 8)

- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [GEOM: Energy-annotated molecular conformations for property prediction and molecular generation](https://mlsanity.com/paper/2006.05531/) (2020)
- [Molecular geometry prediction using a deep generative graph neural network](https://mlsanity.com/paper/1904.00314/) (2019)
- [Learning Neural Generative Dynamics for Molecular Conformation Generation](https://mlsanity.com/paper/2102.10240/) (2021)
- [A Generative Model for Molecular Distance Geometry](https://mlsanity.com/paper/1909.11459/) (2019)
- [HamNet: Conformation-Guided Molecular Representation with Hamiltonian Neural Networks](https://mlsanity.com/paper/2105.03688/) (2021)
- [Auto-Encoding Molecular Conformations](https://mlsanity.com/paper/2101.01618/) (2021)

## Abstract (arXiv)

Straight-forward conformation generation models, which generate 3-D structures directly from input molecular graphs, play an important role in various molecular tasks with machine learning, such as 3D-QSAR and virtual screening in drug design. However, existing loss functions in these models either cost overmuch time or fail to guarantee the equivalence during optimization, which means treating different items unfairly, resulting in poor local geometry in generated conformation. So, we propose Equivalent Distance Geometry Error (EDGE) to calculate the differential discrepancy between conformations where the essential factors of three kinds in conformation geometry (i.e. bond lengths, bond angles and dihedral angles) are equivalently optimized with certain weights. And in the improved version of our method, the optimization features minimizing linear transformations of atom-pair distances within 3-hop. Extensive experiments show that, compared with existing loss functions, EDGE performs effectively and efficiently in two tasks under the same backbones.