2026

Jalalypour, Farzaneh & Mercado, Rocío. (2026) "Chameleonicity Beyond Compactness: Conformational Persistence and Passive Permeability Across 20 PROTAC Ensembles." bioRxiv. (📝 Pre-print) (💻 Code) (📊 Data)

Hudec, Lukáš & Mercado, Rocío. (2026) "The Challenges of PROTAC Permeability Prediction." arXiv. (📝 Pre-print) (💻 Code)

Cropsal, Télio & Mercado, Rocío. (2026) "Can phenotypic activity be predicted without experimental readouts?." arXiv. (📝 Pre-print) (💻 Code)

Voinarovska, Varvara et al. (2026) "Do humans and large language models agree on the quality of synthesis plans?." Digital Discovery. (📄 Paper) (📝 Pre-print) (💻 Code)

Lederbauer, Magdalena et al. (2026) "LeMat-Synth: a multi-modal toolbox to curate broad synthesis procedure databases from scientific literature." arXiv. (📝 Pre-print) (📜 Documentation) (💻 Code) (📊 Data) (📚 Paper corpus)

Granqvist, Emma et al. (2026) "Designing a Robust LLM-Based Evaluation System for Agentic AI in Drug Discovery Through Human Alignment." arXiv. (📝 Pre-print)

Moqvist, Selma et al. (2026) "Boltzmann-Expected Molecular Design with Decoupled Annealing Flows." arXiv. (📝 Pre-print)

Zhang, Zhan-Yun et al. (2026) "Unlocking the Chemical Space for Rechargeable Batteries with a Generative Solvent Design System." ACS Nano. (📄 Paper) (📝 Pre-print)

Andrekson, Leo et al. (2026) "AI-guided discovery for low-resource peptide engineering using evolutionary scale modeling." bioRxiv. (📝 Pre-print)

Zhang, Zhan-Yun et al. (2026) "AI-Accelerated Design and Modeling of Organic Electrochemical Energy Materials: From Redox-Active Molecules to Polymer Electrolytes." Macromol. Mater. Eng.. (📄 Paper) (📝 Pre-print) (🔋 Additional data)

Harrison, Philip John & Mercado, Rocío. (2026) "Biologically-driven generative chemistry: using biological data to guide de novo drug design." ChemRxiv. (📝 Pre-print) (💻 Code)

Larsson, Sofia et al. (2026) "Computational Identification of Active Drug Metabolites for Human Protein Targets." Mol. Pharm.. (📄 Paper) (📝 Pre-print) (💻 Code)

Ribes, Stefano et al. (2026) "TACK: A statistical evaluation of degradation activity on a novel TArgeting Chimeras Knowledge dataset." KDD 2026. (📄 Paper) (📝 Pre-print)

Rao, Yaochen et al. (2026) "Beyond Manual Curation: Augmenting Targeted Protein Degradation Databases via Agentic Literature Extraction Workflows." arXiv. (📝 Pre-print) (💻 Code)

Martínez Crespo, Pablo et al. (2026) "QT-Net: Rethinking Evaluation of AI Models in Atomic Chemical Space." arXiv. (📝 Pre-print) (💻 Code)

Beckmann, Richard et al. (2026) "A unified experimental-simulation dataset and surrogate models for surfactant property prediction." ChemRxiv. (📝 Pre-print)

Ribes, Stefano et al. (2026) "PROTAC-Splitter: a machine learning framework for automated identification of PROTAC substructures." J. Cheminf.. (📄 Paper) (📝 Pre-print) (💻 Code) (📊 Data)

Mannan, Sajid et al. (2026) "Sustainable Materials Discovery in the Era of Artificial Intelligence." arXiv. (📝 Pre-print)

Kazemi-Khasragh, Elaheh et al. (2026) "Descriptor and Graph-based Molecular Representations in Prediction of Copolymer Properties Using Machine Learning." Comput. Mater. Sci.. (📄 Paper) (📝 Pre-print)

2025

Betala, Siddharth et al. (2025) "LeMat-GenBench: A Unified Evaluation Framework for Crystal Generative Models." arXiv. (📝 Pre-print)

Granqvist, Emma et al. (2025) "RetroSynFormer: Planning multi-step chemical synthesis routes via a Decision Transformer." Digital Discovery. (📄 Paper) (📝 Pre-print) (💻 Code)

Ohlsson, Philip Ivers et al. (2025) "Prediction of Permeability and Efflux Using Multitask Learning." ACS Omega. (📄 Paper)

Dunlop, Nils & Erazo, Francisco et al. (2025) "Predicting PROTAC-Mediated Ternary Complexes with AlphaFold3 and Boltz-1." Digital Discovery. (📄 Paper) (📝 Pre-print) (💻 Code) (📊 Data)

Larsson, Sofia & Carlsson, Miranda et al. (2025) "LAGOM: A Transformer-Based Chemical Language Model for Drug Metabolite Prediction." AILSCI. (📄 Paper) (📝 Pre-print) (💻 Code)

Duval, Alexander et al. (2025) "LeMat-GenBench: Bridging the Gap Between Crystal Generation and Materials Discovery." AI4Mat @ NeurIPS 2025. (📄 Paper)

Martínez Crespo, Pablo et al. (2025) "TopoMole: Topological Message Passing Meets Hyperedge Messages." AI4Mat @ NeurIPS 2025. (📄 Paper)

Cropsal, Télio & Mercado, Rocío. (2025) "Compressing Biology: Evaluating the Stable Diffusion VAE for Phenotypic Drug Discovery." Imageomics @ NeurIPS 2025. (📄 Paper) (💻 Code)

Andrekson, Leo et al. (2025) "Contrastive Learning for Robust Cell Annotation and Representation from Single-Cell Transcriptomics." bioRxiv . (📝 Pre-print) (💻 Code) (📊 Data)

Lizak Johansen, Frederik et al. (2025) "deCIFer: Crystal Structure Prediction from Powder Diffraction Data using Autoregressive Language Models." arXiv. (📝 Pre-print) (💻 Code)

2024

Ribes, Stefano et al. (2024) "Modeling PROTAC Degradation Activity with Machine Learning." AILSCI. 6, 100114. (📄 Paper) (📝 Pre-print) (💻 Code)

Gharbi, Yossra at al. (2024) "A Comprehensive Review of Emerging Approaches in Machine Learning for De Novo PROTAC Design." Digital Discovery ASAP. (📄 Paper)

Andrekson, Leo et al. (2024) "Contrastive Learning for Robust Cell Annotation and Representation from Single-Cell Transcriptomics." bioRxiv . (📝 Pre-print)

Westerlund, Annie M. et al. (2024) "Do Chemformers dream of organic matter? Evaluating a transformer model for multi-step retrosynthesis." J. Chem. Inf. Model. 64, 8, 3021–3033. (📄 Paper)

2023

Westerlund, Annie M. et al. (2023) "Do Chemformers dream of organic matter? Evaluating a transformer model for multi-step retrosynthesis." ChemRxiv. (📝 Pre-print)

Mercado, Rocío et al. (2023) "Data sharing in chemistry: lessons learned and a case for mandating structured reaction data." J. Chem. Inf. Model. 63, 14, 4253–4265. (📄 Paper)

2022

Nori, Divya et al. (2022) "De novo PROTAC design using graph-based deep generative models." AI4Science @ NeurIPS 2022. (📄 Paper)

Romeo Atance, Sara et al. (2022) "De novo drug design using reinforcement learning with graph-based deep generative models." J. Chem. Inf. Model. 62(20), 4863–4872. (📄 Paper)

2021

Gao, Wenhao et al. (2022) "Amortized tree generation for bottom-up synthesis planning and synthesizable molecular design." ICLR 2022. (📄 Paper) (📝 Pre-print)

Viguera Diez, Juan et al. (2021) "A transferable Boltzmann generator for small-molecule conformers." ELLIS ML4Molecules. (📄 Paper)

Mercado, Rocío et al. (2021) "Exploring graph traversal algorithms in graph-based molecular generation." J. Chem. Inf. Model. (📄 Paper) (📝 Pre-print)

Romeo Atance, Sara et al. (2021) "De novo drug design using reinforcement learning with graph-based deep generative models." ChemRxiv. (📝 Pre-print)

Zhang, Jie et al. (2021). "Comparative study of deep generative models on chemical space coverage." J. Chem. Inf. Model. 61, 6, 2572–2581. (📄 Paper)

2020

Mercado, Rocío et al. (2020). "Practical notes on building molecular graph generative models." Applied AI Letters. (📄 Paper) (📝 Pre-print)

Mercado, Rocío et al. (2020). "Graph networks for molecular design." Mach. Learn.: Sci. Technol. (📄 Paper) (📝 Pre-print)

Zhang, Jie et al. (2020). "Comparative study of deep generative models on chemical space coverage." ChemRxiv. (📝 Pre-print)

Mercado, Rocío. (2020). "Using GraphINVENT to generate novel DRD2 actives." Cheminformania. (📄 Paper)

David, Laurianne et al. (2020). "Molecular representations in AI-driven drug discovery: a review and practical guide." J. Cheminf. 12(56). (📄 Paper)

2019

Witherspoon, Velencia J. et al. (2019). "Combined nuclear magnetic resonance and molecular dynamics study of methane adsorption in M₂(dobdc) metal–organic frameworks." J. Phys. Chem. C. 123(19). 12286-12295. (📄 Paper)

2018

Braun, Efrem et al. (2018). "Generating carbon schwarzites via zeolite-templating." PNAS. 115(35). E8116-E8124. (📄 Paper)

Mercado, Rocío et al. (2018). "In silico design of 2D and 3D covalent organic frameworks for methane storage applications." Chem. Mater. 30(15). 5069-5086. (📄 Paper)

Forse, Alexander C. et al. (2018). "Unexpected diffusion anisotropy of carbon dioxide in the metal–organic framework Zn₂(dobpdc)." J. Am. Chem. Soc. 140(5). 1663-1673. (📄 Paper)

2016

Mercado, Rocío et al. (2016). "Force field development from periodic density functional theory calculations for gas separation applications using metal–organic frameworks." J. Phys. Chem. C. 120(23). 12590-12604. (📄 Paper)

2015

Xiang, Zhonghua et al. (2015). "Systematic tuning and multifunctionalization of covalent organic polymers for enhanced carbon capture." J. Am. Chem. Soc. 137(41). 13301-13307. (📄 Paper)

Simon, Cory M. et al. (2015). "Computer-aided search for materials to store natural gas for vehicles." Front. Young Minds. 3-11. (📄 Paper)

Simon, Cory M. et al. (2015). "What are the best materials to separate a xenon/krypton mixture?" Chem. Mater. 27(12). 4459-4475. (📄 Paper)

Simon, Cory M. et al. (2015). "The materials genome in action: identifying the performance limits for methane storage." Energy Environ. Sci. 8. 1190-1199. (📄 Paper)