arXiv:2607. 03787v1 Announce Type: new Abstract: Accurately modeling biomolecular interactions is a central bottleneck in biology and therapeutic discovery.
arXiv:2606. 30170v1 Announce Type: cross Abstract: Generative molecular design is shaped by simple proxy benchmarks for drug-like properties and models pretrained on large pharmaceutical datasets.
arXiv:2607. 19237v1 Announce Type: new Abstract: Designing small molecule ligands that bind with high affinity to specific protein pockets is a fundamental goal in drug discovery, as small molecules constitute a major fraction of approved therapeutics.
arXiv:2607. 09998v1 Announce Type: new Abstract: Macrocyclic peptides are an increasingly important therapeutic modality, but existing computational methods for modeling their structures and properties are limited in scope and do not generalize well across the synthetically accessible chemical space.
arXiv:2506. 14488v2 Announce Type: replace-cross Abstract: Structure-based drug design (SBDD) models are central to modern pharmaceutical research, enabling the rational exploration of protein-ligand interactions at atomic resolution.
Target-specific peptide design requires sequence and structure co-design under full atom geometric constraints. Latent generative frameworks offer an effective route for this problem by compressing fine grained atomic structures into block level latent representations and performing conditional generation in a compact latent space.
arXiv:2607. 28553v1 Announce Type: new Abstract: Predicting the 3D structures of atomic systems is fundamental to advancing material science and drug discovery.
arXiv:2606. 25006v1 Announce Type: new Abstract: Target-specific peptide design requires sequence and structure co-design under full atom geometric constraints.
arXiv:2606. 06717v1 Announce Type: cross Abstract: While generative AI models have demonstrated remarkable success in structure-based drug design, they predominantly rely on deep binding pockets and struggle to sample effective ligands for challenging low-pocketability targets, such as the historically "undruggable" oncology targets KRAS and MYC.
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:2602. 06020v3 Announce Type: replace Abstract: How do protein structure prediction models fold proteins?
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.
arXiv:2608. 16094v1 Announce Type: new Abstract: Accurate protein structure prediction is fundamental to structural biology because protein structure underlies molecular function and provides a basis for mechanistic interpretation.