Predicting Hydration Free Energies of the FreeSolv Database of Drug-like Molecules with Molecular Density Functional Theory. - Sohvi Luukkonen; Luc Belloni; Daniel Borgis; Maximilien Levesque (J. Chem. Inf. Model., 2020)

Large-Scale Modeling of Sparse Protein Kinase Activity Data. - Sohvi Luukkonen; Erik Meijer 004; Giovanni Tricarico; Johan Hofmans; Pieter F. W. Stouten; Gerard J. P. van Westen; Eelke B. Lenselink (J. Chem. Inf. Model., 2023)

DrugEx: Deep Learning Models and Tools for Exploration of Drug-Like Chemical Space. - Martin Sícho; Sohvi Luukkonen; Helle W. van den Maagdenberg; Linde Schoenmaker; Olivier J. M. Béquignon; Gerard J. P. van Westen (J. Chem. Inf. Model., 2023)

Diverse Hits in De Novo Molecule Design: Diversity-Based Comparison of Goal-Directed Generators. - Philipp Renz; Sohvi Luukkonen; Günter Klambauer (J. Chem. Inf. Model., 2024)

QSPRpred: a Flexible Open-Source Quantitative Structure-Property Relationship Modelling Tool. - Helle W. van den Maagdenberg; Martin Sícho; David Alencar Araripe; Sohvi Luukkonen; Linde Schoenmaker; Michiel Jespers; Olivier J. M. Béquignon; Marina Gorostiola González; Remco L. van den Broek; Andrius Bernatavicius; J. G. Coen van Hasselt; Piet H. Van Der Graaf; et al. (J. Cheminformatics, 2024)

Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences. - Niklas Schmidinger; Lisa Schneckenreiter; Philipp Seidl; Johannes Schimunek; Pieter-Jan Hoedt; Johannes Brandstetter; Andreas Mayr; Sohvi Luukkonen; Sepp Hochreiter; Günter Klambauer (ICLR, 2025)

MHNfs: Prompting In-Context Bioactivity Predictions for Low-Data Drug Discovery. - Johannes Schimunek; Sohvi Luukkonen; Günter Klambauer (J. Chem. Inf. Model., 2025)

Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design. - Alan Kai Hassen; Martin Sícho; Yorick J. van Aalst; Mirjam C. W. Huizenga; Darcy N. R. Reynolds; Sohvi Luukkonen; Andrius Bernatavicius; Djork-Arné Clevert; Antonius P. A. Janssen; Gerard J. P. van Westen; Mike Preuss (J. Cheminformatics, 2025)