用生成模型同时预测分子晶体结构和晶格,提升药物与材料设计效率。
Packora: Systematic Design for Generative Molecular Crystal Structure Prediction

- 基于流模型联合生成原子坐标与晶格,支持多组分及金属有机晶体
- 在6个生成基准上覆盖率达最优,实验结构复现率更高且收敛更快
- 设计可缓存的成对推理机制,适配药物研发与新材料发现场景
分子晶体结构预测(CSP)在制药、农化和有机电子领域至关重要,因分子构象与堆叠方式的微小差异会显著影响材料性能。我们提出Packora,一种基于流的生成模型,可联合预测分子图对应的原子坐标与晶格。该模型支持多组分及有机金属晶体,并可在单一框架内对任意子集的分子构象、立体化学标签和空间群信息进行条件控制。受CCDC CSP盲测启发,我们分别评估生成与排序性能:生成用于衡量生成器质量,排序则在统一弛豫与排序流程下评估端到端表现。系统研究了架构、训练、条件设置、推理与扩展策略,识别出基于可缓存成对推理、训练目标与数值求解器选择、条件随机丢弃以及成对与单体表示平衡扩展的有效设计。Packora在生成与排序基准上均优于基线,在全部六个生成基准上实现最佳匹配预算覆盖率,同时具备更高的实验结构复现率、更低的实验结构排名与更快的排序收敛速度。
原文摘要 · Abstract (English)
Molecular crystal structure prediction (CSP) is important in pharmaceuticals, agrochemicals, and organic electronics, where subtle differences in molecular conformation and packing can strongly affect material properties. We present Packora, a flow-based generative model for molecular CSP that jointly predicts atomic coordinates and the lattice from molecular graphs. Packora supports multi-component and organometallic crystals and can condition on any subset of molecular conformers, stereochemical labels, and space-group information within a single model. Inspired by the CCDC CSP blind test, we evaluate generation and ranking separately, using generation to isolate generator quality and ranking to measure end-to-end performance under a common relaxation and ranking pipeline. We also systematically study architecture, training, conditioning, inference, and scaling, identifying an effective design based on cacheable pairwise reasoning, training objective and numerical solver choices, conditioning dropout, and balanced scaling of pairwise and single representations. Packora outperforms the baselines on both structure generation and ranking benchmarks, achieving the best matched-budget coverage across all six generation benchmarks, as well as higher experimental-form recovery, lower experimental-form ranks, and faster convergence in ranking.
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