arXiv:2510. 24380v2 Announce Type: replace Abstract: Make-on-demand combinatorial synthesis libraries (CSLs) like Enamine REAL have significantly enabled drug discovery efforts.
arXiv:2606. 26657v1 Announce Type: new Abstract: Identifying high-utility candidates from massive discrete spaces under expensive evaluations is a recurring challenge across the sciences, with structure-based drug discovery as a prominent example.
TopU-LBVS is a new multi‑target benchmark for ligand‑based virtual screening that addresses shortcomings of existing datasets by using hard‑negative decoys and a fixed 1:40 active‑to‑decoy ratio. It covers 93 protein targets across seven classes, provides three evaluation protocols (full, low‑data, and mini), and includes curated ChEMBL‑35 bioactivity data with property‑matched, structurally similar decoys. The benchmark demonstrates that performance drops sharply when moving from random‑decoy to hard‑negative evaluation, and it releases data, splits, code, and baseline implementations for reproducible comparison.
TopU-LBVS is a new multi‑target benchmark for ligand‑based virtual screening that addresses shortcomings of previous datasets by using hard‑negative decoys and a fixed 1:40 active‑to‑decoy ratio. It covers 93 protein targets across seven classes, provides three evaluation protocols (full, low‑data, and mini), and includes curated ChEMBL‑35 bioactivity data with property‑matched, structurally similar decoys to reduce shortcut learning. The benchmark comes with released data, fixed splits, evaluation code, and baseline implementations for reproducible comparison of LBVS and molecular representation methods.
arXiv:2505. 08774v2 Announce Type: replace-cross Abstract: Designing molecules that are both property-optimal and readily synthesizable is a central challenge in drug discovery.
OPDiv is a new algorithm that addresses the tradeoff between ranking quality and chemical diversity in virtual screening. It uses integer optimization to select an optimal subset of top‑k compounds that meet a specified diversity threshold, evaluated with fingerprint, shape, and electrostatic metrics. The method demonstrates how to benchmark virtual screening pipelines by comparing their best achievable diverse selections.
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.
arXiv:2607. 13155v1 Announce Type: new Abstract: Generative molecular models can support early drug discovery by proposing new candidate compounds de novo.
The paper introduces PRISMS, a framework that uses expert pairwise rankings of varying fidelity to curate scientific designs without relying on data-intensive regression models. By escalating queries from lower- to higher-fidelity rankers based on Fisher-information, PRISMS improves discovery recall and reduces the number of screening rounds compared to regression-only and non‑escalated ranking methods. In optimization tasks, PRISMS outperforms Bayesian optimization by achieving higher hypervolume.
arXiv:2602.00663v3 Announce Type: replace Abstract: Optimizing molecules to achieve desired properties is a central bottleneck across the chemical sciences, particularly in the pharmaceutical industr...
arXiv:2608. 11483v1 Announce Type: new Abstract: Hit-to-lead optimization requires iterative design of hit analogs across competing potency, selectivity, physicochemical, pharmacokinetic, safety, and synthetic constraints.
arXiv:2608. 19906v1 Announce Type: new Abstract: Accurately ranking active ligands for a target protein pocket from massive chemical libraries remains a central challenge in virtual screening.
arXiv:2606. 13477v1 Announce Type: cross Abstract: Supramolecular chemistry, which includes the study of non-covalent host-guest assemblies, has advanced various applications.