Enhancing automated drug substance impurity structure elucidation from tandem mass spectra through transfer learning and domain knowledge

Emilio Dorigatti, Jonathan Groß, Jonas Kühlborn, Robert Möckel, Frank Maier and Julian Keupp

Digital Discovery, 2025, 4, 2454
DOI: 10.1039/D5DD00115C

A hitchhiker's guide to deep chemical language processing for bioactivity prediction

Rıza Özçelik and Francesca Grisoni

Digital Discovery, 2025, 4, 316
DOI: 10.1039/D4DD00311J

Going beyond SMILES enumeration for data augmentation in generative drug discovery

Helena Brinkmann, Antoine Argante, Hugo ter Steege and Francesca Grisoni

Digital Discovery, 2025, 4, 2752
DOI: 10.1039/D5DD00028A

Enhancing deep chemical reaction prediction with advanced chirality and fragment representation

Fabrizio Mastrolorito, Fulvio Ciriaco, Orazio Nicolotti and Francesca Grisoni

Chem. Commun., 2025, 61, 18344
DOI: 10.1039/D5CC02641E

Machine learning-based design, screening, and activity validation of topoisomerase I inhibitors

Ya-Kun Zhang, Jian-Bo Tong, Jia-Le Li, Rong Wang and Yan-Rong Zeng

Mol Divers, 2025, 30, 2057
DOI: 10.1007/s11030-025-11295-3

Zero shot molecular generation via similarity kernels

Rokas Elijošius, Fabian Zills, Ilyes Batatia, Sam Walton Norwood, Dávid Péter Kovács, Christian Holm and Gábor Csányi

Nat Commun, 2025, 16
DOI: 10.1038/s41467-025-60963-3

Bridging chemical space and biological efficacy: advances and challenges in applying generative models in structural modification of natural products

Chuan-Su Liu, Bing-Chao Yan, Han-Dong Sun, Jin-Cai Lu and Pema-Tenzin Puno

Nat. Prod. Bioprospect., 2025, 15
DOI: 10.1007/s13659-025-00521-y

Computer-aided ionic liquid design for green chemical processes based on molecular simulation and artificial intelligence

Xinyue Pi, Junfeng Lu, Simin Li, Jinliang Zhang, Yanlei Wang and Hongyan He

Separation and Purification Technology, 2025, 361, 131585
DOI: 10.1016/j.seppur.2025.131585

Deep Lead Optimization: Leveraging Generative AI for Structural Modification

Odin Zhang, Haitao Lin, Hui Zhang, Huifeng Zhao, Yufei Huang, Chang-Yu Hsieh, Peichen Pan and Tingjun Hou

J. Am. Chem. Soc., 2024, 146, 31357
DOI: 10.1021/jacs.4c11686

Review of External Field Effects on Electrocatalysis: Machine Learning Guided Design

Lei Wang, Xuyan Zhou, Zihan Luo, Sida Liu, Shengying Yue, Yan Chen and Yilun Liu

Adv Funct Materials, 2024, 34
DOI: 10.1002/adfm.202408870

ACEGEN: Reinforcement Learning of Generative Chemical Agents for Drug Discovery

Albert Bou, Morgan Thomas, Sebastian Dittert, Carles Navarro, Maciej Majewski, Ye Wang, Shivam Patel, Gary Tresadern, Mazen Ahmad, Vincent Moens, Woody Sherman, Simone Sciabola and Gianni De Fabritiis

J. Chem. Inf. Model., 2024, 64, 5900
DOI: 10.1021/acs.jcim.4c00895

PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models

Morgan Thomas, Mazen Ahmad, Gary Tresadern and Gianni de Fabritiis

J Cheminform, 2024, 16
DOI: 10.1186/s13321-024-00866-5

MolDecor: Leveraging Transformers to Decorate Bioactive Molecules for Property Optimization

Dibyajyoti Das, Sarveswara Rao Vangala and Arijit Roy

J. Chem. Inf. Model., 2025, 65, 9937
DOI: 10.1021/acs.jcim.5c01151

Automating Deep Learning-Based Generation and Evaluation of De Novo Chemical Reaction with ChemRxnSAGE

Anis Ismail, Joe Tekli and Brigitte Wex

J. Chem. Inf. Model., 2025, 65, 10945
DOI: 10.1021/acs.jcim.5c01692

Augmenting Large Language Models for Automated Discovery of F-Element Extractants

Baosen Zhang, Thomas J. Summers, Logan J. Augustine, Michael G. Taylor, Andreas Geist, Rebecca Li, Enrique R. Batista, Danny Perez, Ping Yang and Joshua Schrier

J. Am. Chem. Soc., 2026, 148, 5520
DOI: 10.1021/jacs.5c19738

Generative Deep Learning for de Novo Drug Design─A Chemical Space Odyssey

Rıza Özçelik, Helena Brinkmann, Emanuele Criscuolo and Francesca Grisoni

J. Chem. Inf. Model., 2025, 65, 7352
DOI: 10.1021/acs.jcim.5c00641

gSelformer-MV: Multiview, Subgraph-Augmented Group SELFIES Transformer for Molecular Property Prediction

Vadim Korolev, Alexey Andreevich Sorokin and Yuri Kuratov

J. Chem. Inf. Model., 2026, 66, 246
DOI: 10.1021/acs.jcim.5c02342

fragSMILES as a chemical string notation for advanced fragment and chirality representation

Fabrizio Mastrolorito, Fulvio Ciriaco, Maria Vittoria Togo, Nicola Gambacorta, Daniela Trisciuzzi, Cosimo Damiano Altomare, Nicola Amoroso, Francesca Grisoni and Orazio Nicolotti

Commun Chem, 2025, 8
DOI: 10.1038/s42004-025-01423-3

CSMILES: A Compact, Human-Readable SMILES Extension for Conformations

James W. Furness, Kevin B. Moore and Art Bochevarov

J. Chem. Inf. Model., 2025, 65, 10289
DOI: 10.1021/acs.jcim.5c01613

AI-driven transcriptome profile-guided hit molecule generation

Chen Li and Yoshihiro Yamanishi

Artificial Intelligence, 2025, 338, 104239
DOI: 10.1016/j.artint.2024.104239

Bayesian Flow Network Framework for Chemistry Tasks

Nianze Tao and Minori Abe

J. Chem. Inf. Model., 2025, 65, 1178
DOI: 10.1021/acs.jcim.4c01792

Toward clinical translation of AI-Led drug discovery in endometrial cancer

Phat Ky Nguyen, Thi-My-Trang Luong, Xuan Lam Bui and Nguyen Quoc Khanh Le

Expert Review of Anticancer Therapy, 2026, 26, 23
DOI: 10.1080/14737140.2025.2557602

MolMod: a molecular modification platform for molecular property optimization via fragment-based generation

Yao Zhou, Zhipei Sang, Chao Xu, Ze Cao, Kaixiang Xiao, Qian Jia, Yutao He, Haibin Luo and Shuheng Huang

Mol Divers, 2025, 30, 2209
DOI: 10.1007/s11030-025-11342-z

How evaluation choices distort the outcome of generative drug discovery

Rıza Özçelik and Francesca Grisoni

J Cheminform, 2025, 17
DOI: 10.1186/s13321-025-01108-y

Limeade: Let integer molecular encoding aid

Shiqiang Zhang, Christian W. Feldmann, Frederik Sandfort, Miriam Mathea, Juan S. Campos and Ruth Misener

Computers & Chemical Engineering, 2025, 199, 109115
DOI: 10.1016/j.compchemeng.2025.109115

Advancements in Molecular Property Prediction: A Survey of Single and Multimodal Approaches

Tanya Liyaqat, Tanvir Ahmad and Chandni Saxena

Arch Computat Methods Eng, 2026, 33, 613
DOI: 10.1007/s11831-025-10317-5

Tackling the issue of confined chemical space with AI-based de novo drug design and molecular optimization

Alan Talevi, Lucas N. Alberca and Carolina L. Bellera

Expert Opinion on Drug Discovery, 2025, 20, 1405
DOI: 10.1080/17460441.2025.2555275

Structure-Based Generation of 3D Small-Molecule Drugs: Are We There Yet?

Bo Yang, Chijian Xiang, Tongtong Li, Yunong Xu and Jianing Li

J. Med. Chem., 2025, 68, 22756
DOI: 10.1021/acs.jmedchem.5c01706

A Comparative Review of Large Language Models in Engineering with Emphasis on Chemical Engineering Applications

Teck Leong Khoo, Tin Sin Lee, Soo-Tueen Bee, Chi Ma and Yuan-Yuan Zhang

Processes, 2025, 13, 2680
DOI: 10.3390/pr13092680