arXiv:2606. 23830v1 Announce Type: cross Abstract: Molecular surfaces encode the geometric and physicochemical patterns that determine antibody-antigen recognition, central to epitope prediction.
arXiv:2606. 07567v1 Announce Type: cross Abstract: Protein function is largely determined by molecular surface geometry and physicochemical complementarity, yet most protein design methods condition only on backbone structure.
arXiv:2606. 04154v1 Announce Type: cross Abstract: Antibodies neutralize foreign antigens by binding to specific surface regions called epitopes.
arXiv:2605. 21600v2 Announce Type: replace Abstract: Computational antibody CDR design methods condition on antigen structure to generate binding loops.
arXiv:2606. 14217v1 Announce Type: new Abstract: Accurate prediction of protein-ligand binding affinity is essential for structure-based drug discovery.
arXiv:2606. 14159v1 Announce Type: new Abstract: Protein-ligand binding affinity (PLA) prediction is critical in drug discovery.
arXiv:2606. 28659v1 Announce Type: cross Abstract: High-fidelity molecular docking simulations can produce biologically relevant estimates of epitope-receptor binding affinity but are computationally expensive and therefore limit the number of candidates that can be screened for vaccine design.
Antibodies are essential proteins that play a central role in immune recognition by binding specific antigen molecules. Although recent protein language models have enabled progress in single-chain protein modeling and generation, they often fall short in antigen-specific antibody design, where effective modeling requires explicit pairing between antibody and antigen, particularly at the epitope level.
arXiv:2607. 20551v1 Announce Type: cross Abstract: Effective molecular representation learning is crucial for accurate molecular property prediction.
arXiv:2607. 20057v1 Announce Type: cross Abstract: Antibodies are essential proteins that play a central role in immune recognition by binding specific antigen molecules.
arXiv:2606. 30902v1 Announce Type: cross Abstract: T cell receptor (TCR)-epitope binding prediction is essential for understanding adaptive immunity and developing immunotherapies.
arXiv:2607. 17412v1 Announce Type: new Abstract: A hallmark of neurodegenerative diseases such as Alzheimer's and Parkinson's is the aberrant aggregation of proteins into amyloid fibrils, and small molecules that selectively bind to these fibrils hold promise as diagnostics, imaging probes, and therapeutics.
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.