arXiv Machine LearningBy Daria A. Ryabchenko (Ligand Pro, Moscow, Russia, Skolkovo Institute of Science and Technology, Artificial Intelligence Center, Moscow, Russia), Pavel Gurevich (Ligand Pro, Moscow, Russia, Skolkovo Institute of Science and Technology, Artificial Intelligence Center, Moscow, Russia), Shamil Kadyrov (Ligand Pro, Moscow, Russia), Daria Frolova (Ligand Pro, Moscow, Russia, Skolkovo Institute of Science and Technology, Artificial Intelligence Center, Moscow, Russia), Kseniia Fedisheva (Ligand Pro, Moscow, Russia), Sergei A. Nikolenko (Ligand Pro, Moscow, Russia), Alexander Shapeev (Ligand Pro, Moscow, Russia, Skolkovo Institute of Science and Technology, Artificial Intelligence Center, Moscow, Russia), Marina A. Pak (Ligand Pro, Moscow, Russia)
HEDGEHOG: Hierarchical Evaluation of Drug Generators Through Rigorous Filtration
arXiv:2607. 13155v1 Announce Type: new Abstract: Generative molecular models can support early drug discovery by proposing new candidate compounds de novo.
Summary generated by The Flow from the publisher's feed. The full article
lives at arXiv Machine Learning.
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:2510. 24380v2 Announce Type: replace Abstract: Make-on-demand combinatorial synthesis libraries (CSLs) like Enamine REAL have significantly enabled drug discovery efforts.
By Aryan Pedawi, Jordi Silvestre-Ryan, Bradley Worley, Darren J Hsu, Kushal S Shah, Elias Stehle, Jingrong Zhang, Izhar Wallach
arXiv:2607. 18144v1 Announce Type: cross Abstract: Structure-based drug design (SBDD) leverages the 3D structure of protein targets, often complemented by other spatial constraints, to generate candidate binding molecules.
By Thomas MacDougall, Maksim Kuznetsov, Roman Schutski, Rim Shayakhmetov, Maxim Malkov, Vladimir Aladinskiy, Alex Aliper, Alex Zhavoronkov
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. 00555v1 Announce Type: new Abstract: Structure-based drug design increasingly employs LLM agents to iteratively refine ligands against a target pocket, yet a viable ligand must satisfy two often-conflicting objectives -- binding affinity and druggability -- which single optimization steps rarely improve together.
By Zaifei Yang, Weiyu Chen, Yaqing Wang, James Kwok