PROTAC-Splitter: a machine learning framework for automated identification of PROTAC substructures.

Rocío Mercado

Stefano Ribes Ranxuan Zhang Télio Cropsal Anders Källberg Christian Tyrchan Eva Nittinger Rocío Mercado PROTAC-Splitter: a machine learning framework for automated identification of PROTAC substructures. 2026 December 30 18 J. Cheminformatics 1 https://doi.org/10.1186/s13321-025-01135-9 db/journals/jcheminf/jcheminf18.html#RibesZCKTNM26 streams/journals/jcheminf

Sajid Mannan Rupert J. Myers Rohit Batra Rocío Mercado Lothar Wondraczek N. M. Anoop Krishnan Sustainable Materials Discovery in the Era of Artificial Intelligence. 2026 January abs/2601.21527 CoRR https://doi.org/10.48550/arXiv.2601.21527 db/journals/corr/corr2601.html#abs-2601-21527 streams/journals/corr

Frederik L. Johansen Ulrik Friis-Jensen Erik Bjørnager Dam Kirsten M. Ø. Jensen Rocío Mercado Raghavendra Selvan deCIFer: Crystal Structure Prediction from Powder Diffraction Data using Autoregressive Language Models. 2025 February abs/2502.02189 CoRR https://doi.org/10.48550/arXiv.2502.02189 db/journals/corr/corr2502.html#abs-2502-02189 streams/journals/corr

Télio Cropsal Rocío Mercado Compressing Biology: Evaluating the Stable Diffusion VAE for Phenotypic Drug Discovery. 2025 October abs/2510.19887 CoRR https://doi.org/10.48550/arXiv.2510.19887 db/journals/corr/corr2510.html#abs-2510-19887 streams/journals/corr

Siddharth Betala Samuel P. Gleason Ali Ramlaoui Andy Xu Georgia Channing Daniel Levy 0001 Clémentine Fourrier Nikita Kazeev Chaitanya K. Joshi Sékou-Oumar Kaba Félix Therrien Alex Hernández-García Rocío Mercado N. M. Anoop Krishnan Alexandre Duval LeMat-GenBench: A Unified Evaluation Framework for Crystal Generative Models. 2025 December abs/2512.04562 CoRR https://doi.org/10.48550/arXiv.2512.04562 db/journals/corr/corr2512.html#abs-2512-04562 streams/journals/corr

Annie M. Westerlund Siva Manohar Koki Supriya Kancharla Alessandro Tibo Lakshidaa Saigiridharan Mikhail Kabeshov Rocío Mercado Samuel Genheden Do Chemformers Dream of Organic Matter? Evaluating a Transformer Model for Multistep Retrosynthesis. 3021-3033 2024 64 J. Chem. Inf. Model. 8 https://doi.org/10.1021/acs.jcim.3c01685 db/journals/jcisd/jcisd64.html#WesterlundKKTSKMG24

Yossra Gharbi Rocío Mercado A Comprehensive Review of Emerging Approaches in Machine Learning for De Novo PROTAC Design. 2024 abs/2406.16681 CoRR https://doi.org/10.48550/arXiv.2406.16681 db/journals/corr/corr2406.html#abs-2406-16681 streams/journals/corr

Rocío Mercado Steven M. Kearnes Connor W. Coley Data Sharing in Chemistry: Lessons Learned and a Case for Mandating Structured Reaction Data. 4253-4265 2023 July 63 J. Chem. Inf. Model. 14 https://doi.org/10.1021/acs.jcim.3c00607 db/journals/jcisd/jcisd63.html#MercadoKC23

Rocío Mercado Esben Jannik Bjerrum Ola Engkvist Exploring Graph Traversal Algorithms in Graph-Based Molecular Generation. 2093-2100 2022 62 J. Chem. Inf. Model. 9 https://doi.org/10.1021/acs.jcim.1c00777 db/journals/jcisd/jcisd62.html#MercadoBE22

Sara Romeo Atance Juan Viguera Diez Ola Engkvist Simon Olsson Rocío Mercado <i>De Novo</i> Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models. 4863-4872 2022 62 J. Chem. Inf. Model. 20 https://doi.org/10.1021/acs.jcim.2c00838 db/journals/jcisd/jcisd62.html#AtanceDEOM22

Wenhao Gao 0001 Rocío Mercado Connor W. Coley Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design. 2022 ICLR https://openreview.net/forum?id=FRxhHdnxt1 conf/iclr/2022 db/conf/iclr/iclr2022.html#GaoMC22

Divya Nori Connor W. Coley Rocío Mercado De novo PROTAC design using graph-based deep generative models. 2022 abs/2211.02660 CoRR https://doi.org/10.48550/arXiv.2211.02660 db/journals/corr/corr2211.html#abs-2211-02660

Jie Zhang 0089 Rocío Mercado Ola Engkvist Hongming Chen 0001 Comparative Study of Deep Generative Models on Chemical Space Coverage. 2572-2581 2021 61 J. Chem. Inf. Model. 6 https://doi.org/10.1021/acs.jcim.0c01328 db/journals/jcisd/jcisd61.html#ZhangMEC21

Rocío Mercado Tobias Rastemo Edvard Lindelöf Günter Klambauer Ola Engkvist Hongming Chen 0001 Esben Jannik Bjerrum Graph networks for molecular design. 25023 2021 2 Mach. Learn. Sci. Technol. 2 https://doi.org/10.1088/2632-2153/abcf91 db/journals/mlst/mlst2.html#MercadoRLKECB21

Wenhao Gao 0001 Rocío Mercado Connor W. Coley Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design. 2021 abs/2110.06389 CoRR https://arxiv.org/abs/2110.06389 db/journals/corr/corr2110.html#abs-2110-06389

Laurianne David Amol Thakkar Rocío Mercado Ola Engkvist Molecular representations in AI-driven drug discovery: a review and practical guide. 56 2020 12 J. Cheminformatics 1 https://doi.org/10.1186/s13321-020-00460-5 https://www.wikidata.org/entity/Q108848751 db/journals/jcheminf/jcheminf12.html#DavidTME20

Sara Romeo Atance Rohit Batra Siddharth Betala Esben Jannik Bjerrum Georgia Channing Hongming Chen 0001 Connor W. Coley Télio Cropsal Erik DamErik Bjørnager Dam Laurianne David Juan Viguera Diez Alexandre Duval Ola Engkvist Clémentine Fourrier Ulrik Friis-Jensen Wenhao Gao 0001 Samuel Genheden Yossra Gharbi Samuel P. Gleason Alex Hernández-García Kirsten M. Ø. Jensen Frederik L. Johansen Chaitanya K. Joshi Sékou-Oumar Kaba Mikhail Kabeshov Anders Källberg Supriya Kancharla Nikita Kazeev Steven KearnesSteven M. Kearnes Günter Klambauer Siva Manohar Koki N. M. Anoop Krishnan Daniel Levy 0001 Edvard Lindelöf Sajid Mannan Rupert J. Myers Eva Nittinger Divya Nori Simon Olsson Ali Ramlaoui Tobias Rastemo Stefano Ribes Lakshidaa Saigiridharan Raghavendra Selvan Amol Thakkar Félix Therrien Alessandro Tibo Christian Tyrchan Annie M. Westerlund Lothar Wondraczek Andy Xu Jie Zhang 0089 Ranxuan Zhang