arXiv:2606. 27440v1 Announce Type: new Abstract: Foundation models for structural biology have achieved remarkable performance in predicting biomolecular structure and show promise for the design of proteins and small molecules.
arXiv:2605. 01625v3 Announce Type: replace Abstract: Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology.
arXiv:2606. 02629v1 Announce Type: cross Abstract: Protein-protein interactions (PPIs) are essential for many biological processes.
arXiv:2602. 06020v3 Announce Type: replace Abstract: How do protein structure prediction models fold proteins?
arXiv:2506. 13196v5 Announce Type: replace Abstract: Accurate prediction of protein-ligand binding affinity is critical for drug discovery.
arXiv:2607. 03787v1 Announce Type: new Abstract: Accurately modeling biomolecular interactions is a central bottleneck in biology and therapeutic discovery.
arXiv:2604. 06336v2 Announce Type: replace-cross Abstract: Fragment-level representations provide a natural way to capture recurring molecular substructures and reuse their learned representations across molecules.
arXiv:2608. 09099v1 Announce Type: new Abstract: Quantitative estimation of protein-ligand binding affinity from three-dimensional complex structures is a fundamental task in structure-based computational chemistry and molecular modeling.
arXiv:2607. 01627v1 Announce Type: cross Abstract: Accurate protein-protein interaction (PPI) prediction is central to functional genomics, disease mechanism discovery, and drug development.
arXiv:2606. 10080v1 Announce Type: cross Abstract: Generative models have shown remarkable progress in a variety of domains such as protein design, but such power enables the opaque generation of hazardous proteins.
arXiv:2606. 19374v1 Announce Type: cross Abstract: Graph-based representations are widely used in protein modeling, yet many existing approaches rely primarily on sequence adjacency or geometric proximity, which only partially reflect the principles governing protein folding.
arXiv:2608. 02688v1 Announce Type: cross Abstract: Phenotypic drug discovery enables the discovery of functional relationships between molecular structures and cellular responses.
arXiv:2512. 15133v3 Announce Type: replace-cross Abstract: Proteins inherently possess a consistent sequence-structure duality.