arXiv:2504. 13853v2 Announce Type: replace-cross Abstract: Rational design of lipid nanoparticles (LNPs) for tissue-specific delivery critically depends on predicting the composition of the protein corona that forms on the lipid surface after intravenous administration.
arXiv:2507. 03209v2 Announce Type: replace-cross Abstract: The discovery of new ionizable lipids for efficient lipid nanoparticle (LNP)-mediated RNA delivery remains a major bottleneck in RNA therapeutics development.
arXiv:2505. 20346v3 Announce Type: replace-cross Abstract: Function-guided protein design is a crucial task with significant applications in drug discovery and enzyme engineering.
The paper introduces NSA-Bench, a public benchmark for predicting nano self‑assembly (NSA) between molecular pairs, framing it as a binary classification problem. It presents NSA‑Net, a multimodal learning framework that fuses graph topology, sequence semantics, and physicochemical descriptors to predict self‑assembly, achieving high ROC‑AUC scores and outperforming existing baselines. The study also demonstrates how NSA‑Net’s predictions can guide experimental formulation refinement through an NSA‑Agent case study.
The paper introduces LambdaDockScore, a protein‑protein docking scoring function that leverages the LambdaLoss loss from Learning‑to‑Rank to improve pose ranking. By fine‑tuning the energy prediction head of DFMDock on 2.9 million decoy poses from the DIPS dataset, LambdaDockScore outperforms the state‑of‑the‑art EuDockScore on CAPRI benchmark targets, achieving higher accuracy in top‑1 and top‑5 predictions. It also enhances ranking for antibody‑antigen and protein‑protein complexes with extreme binding interface sizes.
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. 31126v1 Announce Type: new Abstract: Predicting biomolecular properties from limited labeled data is a central bottleneck in protein engineering and small-molecule design.
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: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:2608. 04257v1 Announce Type: new Abstract: Blood-brain barrier permeability (BBBP) prediction is a critical screening task in central nervous system drug discovery, where candidate molecules must be assessed for whether they can cross, or should be prevented from crossing, the blood-brain barrier.
arXiv:2606. 13477v1 Announce Type: cross Abstract: Supramolecular chemistry, which includes the study of non-covalent host-guest assemblies, has advanced various applications.
The paper proposes a three‑stage training pipeline that begins with procedural pretraining on abstract, procedurally generated data, followed by molecular pretraining on SMILES, and finally downstream fine‑tuning for molecular property prediction. Experiments show that procedural pretraining improves downstream performance—e.g., a 4.8% error reduction on Lipophilicity—especially when labeled data are scarce, and that the benefit peaks at an intermediate procedural training budget. Analysis indicates that transferable knowledge resides mainly in attention layers, while feed‑forward layers may over‑specialize.
arXiv:2608.29207v1 Announce Type: new Abstract: Protein structure modeling rests on a single computational primitive: the interaction between what a residue is (sequence content) and where it sits (t...