arXiv:2607. 12349v1 Announce Type: new Abstract: Drug discovery and development is time-consuming and resource-intensive, motivating computational approaches such as diffusion models for de novo drug design.
By Ruoxi Gao, Jiangweizhi Peng, Ziqi Chen, Frazier N. Baker, David C. Kombo, John L. Kane Jr., Andrew A. Scholte, Yi Li, Matthew J. LaMarche, Luigi I. Iconaru, Hans-Peter Biemann, Mingyi Hong, Xia Ning
Drug discovery and development is time-consuming and resource-intensive, motivating computational approaches such as diffusion models for de novo drug design. Many such models follow the structure-based drug design (SBDD) paradigm, generating molecules to fit a target binding pocket.
arXiv:2606. 01220v1 Announce Type: cross Abstract: Generating molecules that simultaneously satisfy drug-like properties and conform to the 3D structure of a target protein is a core challenge in structure-based drug design (SBDD).
By Guang Lin, Shikui Tu, Lei Xu
arXiv:2607. 01105v1 Announce Type: new Abstract: We present SynLaD, a latent diffusion framework for small-molecule generation that unifies ligand-based drug design objectives (what to make) with synthetic accessibility (how to make it).
By Miruna Cretu, John Bradshaw, Patricia Suriana, Saeed Saremi, Omar Mahmood, Kirill Shmilovich, Kangway Chuang, Vishnu Sresht, Colin Grambow
arXiv:2607. 08404v1 Announce Type: cross Abstract: Current computational approaches for drug design typically focus on generating molecules conditioned on specific targets or general molecular properties, often neglecting the influence of disease context on target behavior and therapeutic outcomes.
By Ali Motahharynia, Mohammadreza Ghaffarzadeh-Esfahani, Mahsa Sheikholeslami, Navid Mazrouei, Matin Irajpour, Yousof Gheisari, Hajar Sirous
arXiv:2606. 02902v1 Announce Type: cross Abstract: Deep reinforcement learning (DRL) is increasingly applied to de novo molecular design, but choices in data, rewards, and evaluation can yield uneven performance across disease areas and chemotypes.
By Esmaeil Shakeri, Ronnie de Souza Santos, Behrouz Far
arXiv:2509. 26405v2 Announce Type: replace Abstract: We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules.
By Benno Kaech, Luis Wyss, Karsten Borgwardt, Gianvito Grasso
arXiv:2606. 23856v1 Announce Type: new Abstract: Generative molecular models for drug design are a promising direction with much active research.
By Konstantin Yatsenko, Arvind Thiagarajan
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.
By Dong Xu, Zhangfan Yang, Junchuang Cai, Sisi Yuan, Zexuan Zhu, Jianqiang Li, Junkai Ji
arXiv:2511. 19264v2 Announce Type: replace-cross Abstract: Generative Flow Networks (GFlowNets) construct molecules through sequential decisions, but their internal policies remain opaque, limiting adoption in drug discovery, where chemists need interpretable rationales for proposed structures.
By Amirtha Varshini A S, Duminda S. Ranasinghe, Hok Hei Tam
arXiv:2608. 14293v1 Announce Type: cross Abstract: High-content microscopy enables systematic profiling of cellular responses to chemical perturbations, but the scale of the chemical space makes exhaustive phenotypic characterization experimentally infeasible.
By Gauthier Avit\'e, Maxime Sanchez-Renauld, Nicolas Bourriez, Auguste Genovesio
arXiv:2605. 25681v2 Announce Type: replace-cross Abstract: Designing a single molecule that modulates two targets is a promising strategy for polypharmacology, but it remains substantially harder than standard single-target generation because one candidate must satisfy two binding requirements while preserving drug-likeness and synthesizability.
By Qingyuan Zeng, Pengxiang Cai, Zixin Guan, Ziyang Chen, Anglin Liu, Xinyao Lai, Jintai Chen