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Packora is a flow-based generative model designed for molecular crystal structure prediction (CSP). It jointly predicts atomic coordinates and lattice parameters from molecular graphs, supporting multi-component and organometallic crystals and allowing conditioning on conformers, stereochemistry, and space-group data. In evaluations inspired by the CCDC CSP blind test, Packora outperforms baselines on generation and ranking benchmarks, achieving superior matched-budget coverage, higher experimental-form recovery, lower ranks, and faster convergence.
The paper introduces CG-OMatG, an equivariant Riemannian flow-based generative model that predicts molecular crystal structures using a coarse-grained, hierarchical representation. It treats molecules as rigid bodies, performs inter- and intra-molecular message passing, and learns to reconstruct molecule centroids, orientations, and lattice parameters conditioned on chemical species and conformer geometry. The model is trained on OMC25 and CSD datasets, fine-tuned with policy gradient reinforcement learning to favor low-energy structures, and validated against a CSP blind test benchmark using COMPACK packing-similarity analysis.
The study benchmarks 12 deep generative crystal structure prediction models against the template-based TCSP 2.0 on 180 test structures, finding that template retrieval achieves the highest top‑1 success (68.3%). Most generative predictions overlap with template substitutions, and removing entire stoichiometric prototype families from training reduces accuracy by 50‑78%, indicating strong prototype dependence. Only a small subset of predictions remain after such removal, suggesting limited genuine de‑novo capability.
AtomSteer is a test‑time inference framework that steers pretrained atomistic generative models to satisfy structural constraints such as crystallographic symmetry, geometry, and stereochemistry. It applies bounded local projections, graph‑rigid stereochemical transformations, and periodic symmetry projections during sampling, accepting updates that improve constraint satisfaction while preserving the rest of the structure. The method is demonstrated on three backbones—FlowMM, ET‑Flow, and Boltz‑2—across tasks including de novo crystal generation, crystal structure prediction, molecular conformer generation, and protein‑ligand complex prediction, yielding improvements in space‑group coverage, stereochemical accuracy, and ligand E/Z error rates.
arXiv:2606. 03199v1 Announce Type: new Abstract: Organic crystal structure prediction (CSP) is a requirement for computational modelling of organic solids, but traditionally costs several CPU-years per molecule.
arXiv:2601. 09285v2 Announce Type: replace Abstract: Metal-organic frameworks (MOFs) are porous crystalline materials with broad applications such as carbon capture and drug delivery, yet accurately predicting their 3D structures remains a significant challenge.