Supervised machine learning techniques are increasingly being adopted to speed up electronic structure predictions, serving as alternatives to first-principles methods like Density Functional Theory (DFT). Although current DFT datasets mainly emphasize chemical properties and atomic forces, the precise prediction of electronic charge density is essential for accurately determining a system's total energy and ground state properties. In this study, we introduce a novel electronic charge density dataset named ECD, which encompasses 140,646 stable crystal geometries with medium-precision Perdew–Burke–Ernzerhof (PBE) functional data. Within this dataset, a subset of 7,147 geometries includes high-precision electronic charge density data calculated using the Heyd–Scuseria–Ernzerhof (HSE) functional in DFT. By designing various benchmark tasks for crystalline materials and emphasizing training with large-scale PBE data while fine-tuning with a smaller subset of high-precision HSE data, we demonstrate the efficacy of current machine learning models in predicting electronic charge densities. The ECD dataset and baseline models are open-sourced to support community efforts in developing new methodologies and accelerating materials design and applications.

In addressing the challenge of Crystal Structure Prediction (CSP), symmetry-aware deep learning models, particularly diffusion models, have been extensively studied, which treat CSP as a conditional generation task. However, ensuring permutation, rotation, and periodic translation equivariance during diffusion process remains incompletely addressed. In this work, we propose EquiCSP, a novel equivariant diffusion-based generative model. We not only address the overlooked issue of lattice permutation equivariance in existing models, but also develop a unique noising algorithm that rigorously maintains periodic translation equivariance throughout both training and inference processes. Our experiments indicate that EquiCSP significantly surpasses existing models in terms of generating accurate structures and demonstrates faster convergence during the training process.

Superconductivity is a fascinating phenomenon observed in certain materials under certain conditions. However, some critical aspects of it, such as the relationship between superconductivity and materials' chemical/structural features, still need to be understood. Recent successes of data-driven approaches in material science strongly inspire researchers to study this relationship with them, but a corresponding dataset is still lacking. Hence, we present a new dataset for data-driven approaches, namely SuperCon3D, containing both 3D crystal structures and experimental superconducting transition temperature (Tc) for the first time. Based on SuperCon3D, we propose two deep learning methods for designing high Tc superconductors. The first is SODNet, a novel equivariant graph attention model for screening known structures, which differs from existing models in incorporating both ordered and disordered geometric content. The second is a diffusion generative model DiffCSP-SC for creating new structures, which enables high Tc-targeted generation. Extensive experiments demonstrate that both our proposed dataset and models are advantageous for designing new high Tc superconducting candidates.

SUMMARY: VSTH is a user-friendly web server with the complete workflow for virtual screening. By self-customized visualization software, users can interactively prepare protein files, set docking sites as well as view binding conformers in a target protein in a few clicks. We provide serval purchasable ligand libraries for selection. And, we integrate six open-source docking programs as computing engine, or as conformational sampling tools for DLIGAND2. Users can select various docking methods simultaneously and personalize computing parameters. After docking processing, user can filter docking conformations by ranked scores, or cluster-based molecular similarity to find highly populated clusters of low-energy conformations. AVAILABILITY AND IMPLEMENTATION: The VSTH web server is free and open to all users at https://matgen.nscc-gz.cn/VirtualScreening.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.