APBIO: bioactive profiling of air pollutants through inferred bioactivity signatures and prediction of novel target interactions by Eva Viesi, Ugo Perricone, Patrick Aloy, Rosalba Giugno

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Context-dependent similarity analysis of analogue series for structure–activity relationship transfer based on a concept from natural language processing by Atsushi Yoshimori, Jürgen Bajorath

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Fragmenstein: predicting protein–ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding–based methodology by Matteo P. Ferla, Rubén Sánchez-García, Rachael E. Skyner, Stefan Gahbauer, Jenny C. Taylor, Frank von Delft, Brian D. Marsden, Charlotte M. Deane

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hERGAT: predicting hERG blockers using graph attention mechanism through atom- and molecule-level interaction analyses by Dohyeon Lee, Sunyong Yoo

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MLinvitroTox reloaded for high-throughput hazard-based prioritization of high-resolution mass spectrometry data by Katarzyna Arturi, Eliza J. Harris, Lilian Gasser, Beate I. Escher, Georg Braun, Robin Bosshard, Juliane Hollender

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The algebraic extended atom-type graph-based model for precise ligand–receptor binding affinity prediction by Farjana Tasnim Mukta, Md Masud Rana, Avery Meyer, Sally Ellingson, Duc D. Nguyen

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Chemical space as a unifying theme for chemistry by Jean-Louis Reymond

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CIME4R: Exploring iterative, AI-guided chemical reaction optimization campaigns in their parameter space by Christina Humer, Rachel Nicholls, Henry Heberle, Moritz Heckmann, Michael Pühringer, Thomas Wolf, Maximilian Lübbesmeyer, Julian Heinrich, Julius Hillenbrand, Giulio Volpin, Marc Streit

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Positional embeddings and zero-shot learning using BERT for molecular-property prediction by Medard Edmund Mswahili, JunHa Hwang, Jagath C. Rajapakse, Kyuri Jo, Young-Seob Jeong

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One size does not fit all: revising traditional paradigms for assessing accuracy of QSAR models used for virtual screening by James Wellnitz, Sankalp Jain, Joshua E. Hochuli, Travis Maxfield, Eugene N. Muratov, Alexander Tropsha, Alexey V. Zakharov

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Matched pairs demonstrate robustness against inter-assay variability by Jochem Nelen, Horacio Pérez-Sánchez, Hans De Winter, Dries Van Rompaey

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AiGPro: a multi-tasks model for profiling of GPCRs for agonist and antagonist by Rahul Brahma, Sunghyun Moon, Jae-Min Shin, Kwang-Hwi Cho

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PretoxTM: a text mining system for extracting treatment-related findings from preclinical toxicology reports by Javier Corvi, Nicolás Díaz-Roussel, José M. Fernández, Francesco Ronzano, Emilio Centeno, Pablo Accuosto, Celine Ibrahim, Shoji Asakura, Frank Bringezu, Mirjam Fröhlicher, Annika Kreuchwig, Yoko Nogami, Jeong Rih, Raul Rodriguez-Esteban, Nicolas Sajot, Joerg Wichard, Heng-Yi Michael Wu, Philip Drew, Thomas Steger-Hartmann, Alfonso Valencia, Laura I. Furlong, Salvador Capella-Gutierrez

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Barlow Twins deep neural network for advanced 1D drug–target interaction prediction by Maximilian G. Schuh, Davide Boldini, Annkathrin I. Bohne, Stephan A. Sieber

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Improving drug repositioning with negative data labeling using large language models by Milan Picard, Mickael Leclercq, Antoine Bodein, Marie Pier Scott-Boyer, Olivier Perin, Arnaud Droit

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