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.
By Mohammad Haddadnia, Yuvan Chali, Abhilash Jayaraj, Constance Kraay, Joana Reis, Felix Strieth-Kalthoff, Haribabu Arthanari
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.
By Jeff Guo, V\'ictor Sabanza-Gil, Olha Semenenko, Oleksii Hrabovskyi, Mykola Protopopov, Anna Kapeliukha, Oleksandr Mosia, Sofiia Hatych, Diana Alieksieieva, Tom Nelis, Patrick Molliet, Helena Sol\'e-\`Avila, Valentas Olikauskas, Nina Aregger, Irina Morozova, Joseph Schmidt, Zlatko Jon\v{c}ev, Olga Tarkhanova, Petro Borysko, Jerome Waser, Bruno Correia, Jeremy Luterbacher, Philippe Schwaller
arXiv:2607. 13155v1 Announce Type: new Abstract: Generative molecular models can support early drug discovery by proposing new candidate compounds de novo.
By 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)
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.
By Kelvin P. Idanwekhai, Enes Kelestemur, Benjamin Strickland, Matthew Hart, Steini Davidsson, Angelos Angelopoulos, Ron Alterovitz, Marcello DeLuca, Alexander Tropsha
arXiv:2606. 13477v1 Announce Type: cross Abstract: Supramolecular chemistry, which includes the study of non-covalent host-guest assemblies, has advanced various applications.
By Tianyi Ma, Yijun Ma, Zehong Wang, Weixiang Sun, Ziming Li, Connor R. Schmidt, Chuxu Zhang, Matthew J. Webber, Yanfang Ye
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:2608. 17567v1 Announce Type: cross Abstract: Pretrained molecular language models are increasingly used as molecular encoders for learning structure-property relationships.
By Henrik Wille, Luis-Finley Sch\"utz, Felix Strieth-Kalthoff
arXiv:2607. 04774v1 Announce Type: new Abstract: Untargeted tandem mass spectrometry (MS/MS) detects thousands of small molecules per biological sample, yet most go unidentified because they are absent from spectral libraries.
By Xujun Che, Xiuxia Du, Depeng Xu
arXiv:2608. 07454v1 Announce Type: cross Abstract: The total synthesis of a complex molecule is among the most demanding intellectual and experimental feats in chemistry: a chemist must plan many steps ahead for how to assemble simple building blocks into an intricate target, devise backup strategies, and anticipate procedural challenges.
By Daniel Armstrong, Xuan-Vu Nguyen, Octavian Susanu, Gabriel Gibberd, Th\'eo A. Neukomm, Tadd\"aus Strunden, Dan Forster, Morgane Delattre, Shawn Teh, Cl\'ement Rols, John Federice, Hayden Leatherwood, M. Lavelle Barnes, Maarten R. Dobbelaere, Peter Wipf, Jon T. Njardarson, Jieping Zhu, Philippe Schwaller
arXiv:2607. 12488v1 Announce Type: new Abstract: Molecular optimization in drug discovery, materials design, and catalysis requires searching vast chemical spaces under tight evaluation budgets, since high-fidelity oracles and experimental measurements are costly.
By Sarina Kopf, Cristina Nevado, Philippe Schwaller
arXiv:2607. 28437v1 Announce Type: new Abstract: Molecular optimization is commonly performed under a limited oracle budget, which makes deciding what to evaluate as important as deciding what to generate.
By Jiannan Yang, Veronika Thost, Xiang Ling, Tengfei Ma
arXiv:2606. 05198v1 Announce Type: cross Abstract: Nucleic acids are increasingly recognized as therapeutic targets beyond conventional protein-centered drug discovery, yet accurate and efficient docking of small molecules to nucleic acid structures remains challenging.
By Shi Li (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China), Xujun Zhang (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China), Mingquan Liu (Faculty of Health Sciences, University of Macau, Macau SAR, China), Hui Zhang (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Shanghai Innovation Institute, Shanghai, China), Shuoying Jia (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Shanghai Innovation Institute, Shanghai, China), Yu Kang (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Shanghai Innovation Institute, Shanghai, China), Tingjun Hou (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Zhejiang Provincial Key Laboratory for Intelligent Drug Discovery and Development, Jinhua Institute of Zhejiang University, Zhejiang, China), Peichen Pan (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Zhejiang Provincial Key Laboratory for Intelligent Drug Discovery and Development, Jinhua Institute of Zhejiang University, Zhejiang, China)