CryoAtlas is a large, rigorously curated dataset and unified benchmark for density‑guided atomic model building of protein chains from cryo‑EM maps. It compiles 17,809 map‑model‑sequence entries from EMDB and PDB (up to March 2026), with a 16,657‑entry training split, and defines a 618‑target benchmark that evaluates structural accuracy, map fit, and stereochemical validity. The resource enables systematic comparison of learning‑based methods with traditional tools like Phenix and AlphaFold3, and demonstrates that retraining a CNN component on CryoAtlas improves performance.
arXiv:2606. 31332v1 Announce Type: new Abstract: Protein automodeling from cryo-EM density maps faces unique challenges in enforcing physicochemical validity and managing conformational heterogeneity.
arXiv:2606. 00955v1 Announce Type: new Abstract: Despite the growing availability of cryo-electron microscopy (cryo-EM) density maps, effectively leveraging them for protein representation remains challenging.
arXiv:2607. 28553v1 Announce Type: new Abstract: Predicting the 3D structures of atomic systems is fundamental to advancing material science and drug discovery.
Fold'EM is an inference-time framework that directly combines protein generative model priors with cryo‑EM particle images to recover atomic structures, bypassing the traditional density reconstruction step. It can determine structures from a small number of particles, jointly infer orientations in an ab‑initio setting, and resolve distinct conformational states in heterogeneous samples without separate map reconstruction. The method demonstrates accurate atomic models on both synthetic and experimental datasets, showing promise for low‑sample and low‑population conformational analysis.
Large-scale self-supervised pretraining has reshaped modern machine learning, substantially advancing the ability of language and vision models to generalize across downstream tasks. While deep learni...
arXiv:2610.08400v1 Announce Type: cross Abstract: Large-scale self-supervised pretraining has reshaped modern machine learning, substantially advancing the ability of language and vision models to ge...
arXiv:2607. 12380v1 Announce Type: new Abstract: Small molecules, crystals, and proteins all reduce to atoms in 3D space, yet their generative pipelines remain fragmented across domains, each with its Small molecules, crystals, and proteins all reduce to atoms in 3D space, yet their generative pipelines remain fragmented across domains, each with its own graph, equivariant, or frame-based architecture.
Zatom-2 is a multitask generative model for atomistic data that has been pretrained on about five million structures from the OMol25 and OMat24 datasets. It uses a multiscale Transformer with conditional flow matching to support tasks such as generation, structure prediction, and energy/force prediction for both molecules and materials. The model outperforms its predecessor, Zatom-1, on molecular distribution fidelity and benchmark generation tasks, and improves protein backbone designability from 67.8% to 74.8% after finetuning on 2,000 protein domains.
arXiv:2606. 30961v1 Announce Type: cross Abstract: Advances in deep learning architectures and representations have enabled ML-driven chemical property prediction, but state-of-the-art (SOTA) models have remained largely confined to independent codebases and lack support for diverse chemical species.
ProtModernBERT is a modernized BERT-style protein language model that reduces training cost by incorporating architectural refinements, achieving performance comparable to larger models while cutting pre‑training FLOPs by 80‑90%. The authors benchmark ProtModernBERT against ProtBert, Amplify, and ESM2 on supervised structural tasks and a zero‑shot functional benchmark, showing it matches or closely tracks Amplify‑120M and ProtBert. Their cluster‑based validation and random‑init experiments reveal that modern architectural components provide stronger inductive biases than parameter count in low‑compute regimes.
arXiv:2606. 10255v1 Announce Type: cross Abstract: Cryo-electron tomography (cryoET) has emerged as a powerful tool in structural and cellular biology by enabling direct visualization of macromolecular structures within intact cells, thereby linking molecular architecture to cellular organization in a native context.
arXiv:2606. 03232v1 Announce Type: cross Abstract: Graph Neural Networks (GNNs) have revolutionized Neural Force Fields for atomistic simulations, achieving near-quantum accuracy at reduced cost, yet adapting these models to new chemical systems requires expensive retraining of foundation models.