When Single Answer Is Not Enough: Rethinking Single-Step Retrosynthesis Benchmarks for LLMs.

Alex Aliper Alexander Aliper

Bogdan Zagribelnyy Ivan Ilin Maksim Kuznetsov Nikita Bondarev Roman Schutski Thomas MacDougall Rim Shayakhmetov Zulfat Miftakhutdinov Mikolaj Mizera Vladimir Aladinskiy Alex Aliper Alex Zhavoronkov When Single Answer Is Not Enough: Rethinking Single-Step Retrosynthesis Benchmarks for LLMs. 2026 February abs/2602.03554 CoRR https://doi.org/10.48550/arXiv.2602.03554 db/journals/corr/corr2602.html#abs-2602-03554 streams/journals/corr

Maksim Kuznetsov Zulfat Miftahutdinov Rim Shayakhmetov Mikolaj Mizera Roman Schutski Bogdan Zagribelnyy Ivan Ilin Nikita Bondarev Thomas MacDougall Mathieu Reymond Mihir Bafna Kaeli Kaymak-Loveless Eugene Babin Maxim Malkov Mathias Lechner Ramin M. Hasani Alexander Amini Vladimir Aladinskiy Alex Aliper Alex Zhavoronkov MMAI Gym for Science: Training Liquid Foundation Models for Drug Discovery. 2026 March abs/2603.03517 CoRR https://doi.org/10.48550/arXiv.2603.03517 db/journals/corr/corr2603.html#abs-2603-03517 streams/journals/corr

Bogdan Zagribelnyy Ivan Ilin Nikita Bondarev Anton Morgunov Arkadii Lin Maksim Kuznetsov Rim Shayakhmetov Vladimir Aladinskiy Alex Aliper Alex Zhavoronkov URSA: Chemistry-Aware Benchmark for Utilitarian Retrosynthesis Assessment. 2026 July abs/2607.04688 CoRR https://doi.org/10.48550/arXiv.2607.04688 db/journals/corr/corr2607.html#abs-2607-04688 streams/journals/corr

Thomas MacDougall Maksim Kuznetsov Roman Schutski Rim Shayakhmetov Maxim Malkov Vladimir Aladinskiy Alex Aliper Alex Zhavoronkov Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints. 2026 July abs/2607.18144 CoRR https://doi.org/10.48550/arXiv.2607.18144 db/journals/corr/corr2607.html#abs-2607-18144 streams/journals/corr

Maksim Kuznetsov Airat Valiev Alex Aliper Daniil Polykovskiy Elena Tutubalina Rim Shayakhmetov Zulfat Miftahutdinov nach0-pc: Multi-task Language Model with Molecular Point Cloud Encoder. 24357-24365 2025 AAAI https://doi.org/10.1609/aaai.v39i23.34613 conf/aaai/2025 db/conf/aaai/aaai2025.html#KuznetsovVAPTSM25

Tianbiao Yang Xiaoyu Ding Elizabeth McMichael Frank W. Pun Alex Aliper Feng Ren Alex Zhavoronkov Xiao Ding AttenhERG: a reliable and interpretable graph neural network framework for predicting hERG channel blockers. 143 2024 December 16 J. Cheminformatics 1 https://doi.org/10.1186/s13321-024-00940-y db/journals/jcheminf/jcheminf16.html#YangDMPARZD24 streams/journals/jcheminf

Maksim Kuznetsov Fedor Ryabov Roman Schutski Rim Shayakhmetov Yen-Chu Lin Alex Aliper Daniil Polykovskiy COSMIC: Molecular Conformation Space Modeling in Internal Coordinates with an Adversarial Framework. 3610-3620 2024 64 J. Chem. Inf. Model. 9 https://doi.org/10.1021/acs.jcim.3c00989 db/journals/jcisd/jcisd64.html#KuznetsovRSSLAP24

Petrina Kamya Ivan V. Ozerov Frank W. Pun Kyle Tretina Tatyana Fokina Shan Chen Vladimir Naumov Xi Long Sha Lin Mikhail Korzinkin Daniil Polykovskiy Alex Aliper Feng Ren Alex Zhavoronkov PandaOmics: An AI-Driven Platform for Therapeutic Target and Biomarker Discovery. 3961-3969 2024 64 J. Chem. Inf. Model. 10 https://doi.org/10.1021/acs.jcim.3c01619 db/journals/jcisd/jcisd64.html#KamyaOPTFCNLLKPARZ24

Mohammad Ghazi Vakili Christoph Gorgulla AkshatKumar Nigam Dmitry Bezrukov Daniel Varoli Alex Aliper Daniil Polykovskiy Krishna M. Padmanabha Das Jamie Snider Anna Lyakisheva Ardalan Hosseini Mansob Zhong Yao Lela Bitar Eugene Radchenko Xiao Ding Jinxin Liu Fanye Meng Feng Ren Yudong Cao Igor Stagljar Alán Aspuru-Guzik Alex Zhavoronkov Quantum Computing-Enhanced Algorithm Unveils Novel Inhibitors for KRAS. 2024 abs/2402.08210 CoRR https://doi.org/10.48550/arXiv.2402.08210 db/journals/corr/corr2402.html#abs-2402-08210

Maksim Kuznetsov Airat Valiev Alex Aliper Daniil Polykovskiy Elena Tutubalina Rim Shayakhmetov Zulfat Miftahutdinov nach0-pc: Multi-task Language Model with Molecular Point Cloud Encoder. 2024 abs/2410.09240 CoRR https://doi.org/10.48550/arXiv.2410.09240 db/journals/corr/corr2410.html#abs-2410-09240 streams/journals/corr

Yan A. Ivanenkov Daniil Polykovskiy Dmitry Bezrukov Bogdan Zagribelnyy Vladimir Aladinskiy Petrina Kamya Alex Aliper Feng Ren Alex Zhavoronkov Chemistry42: An AI-Driven Platform for Molecular Design and Optimization. 695-701 2023 February 63 J. Chem. Inf. Model. 3 https://doi.org/10.1021/acs.jcim.2c01191 db/journals/jcisd/jcisd63.html#IvanenkovPBZAKARZ23

Po-Yu Kao Ya-Chu Yang Wei-Yin Chiang Jen-Yueh Hsiao Yudong Cao Alex Aliper Feng Ren Alán Aspuru-Guzik Alex Zhavoronkov Min-Hsiu Hsieh Yen-Chu Lin Exploring the Advantages of Quantum Generative Adversarial Networks in Generative Chemistry. 3307-3318 2023 June 63 J. Chem. Inf. Model. 11 https://doi.org/10.1021/acs.jcim.3c00562 https://www.wikidata.org/entity/Q130272837 db/journals/jcisd/jcisd63.html#KaoYCHCARAZHL23

Micha Livne Zulfat Miftahutdinov Elena Tutubalina Maksim Kuznetsov Daniil Polykovskiy Annika Brundyn Aastha Jhunjhunwala Anthony Costa Alex Aliper Alex Zhavoronkov nach0: Multimodal Natural and Chemical Languages Foundation Model. 2023 abs/2311.12410 CoRR https://doi.org/10.48550/arXiv.2311.12410 db/journals/corr/corr2311.html#abs-2311-12410

Feng Ren Xiao Ding Min Zheng Mikhail Korzinkin Xin Cai Wei Zhu Alexey Mantsyzov Alex Aliper Vladimir Aladinskiy Zhongying Cao Shanshan Kong Xi Long Bonnie Hei Man Liu Yingtao Liu Vladimir Naumov Anastasia Shneyderman Ivan V. Ozerov Ju Wang Frank W. Pun Alán Aspuru-Guzik Michael Levitt 0001 Alex Zhavoronkov AlphaFold Accelerates Artificial Intelligence Powered Drug Discovery: Efficient Discovery of a Novel Cyclin-dependent Kinase 20 (CDK20) Small Molecule Inhibitor. 2022 abs/2201.09647 CoRR https://arxiv.org/abs/2201.09647 db/journals/corr/corr2201.html#abs-2201-09647

Vladimir Naumov Evgeny Putin Stefan Pushkov Ekaterina Kozlova Konstantin Romantsov Alexander A. Kalashnikov Fedor Galkin Nina Tihonova Anastasia Shneyderman Egor Galkin Arsenii Zinkevich Stephanie M. Cope Ramanathan Sethuraman Tudor I. Oprea Alexander T. Pearson Savas Tay Nishant Agrawal Alexey Dubovenko Quentin Vanhaelen Ivan Ozerov Alex Aliper Evgeny Izumchenko Alex Zhavoronkov COVIDomic: A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity. 2021 17 PLoS Comput. Biol. 7 https://doi.org/10.1371/journal.pcbi.1009183 https://www.wikidata.org/entity/Q112609840 db/journals/ploscb/ploscb17.html#NaumovPPKRKGTSG21

Yan A. Ivanenkov Alexander Zhebrak Dmitry Bezrukov Bogdan Zagribelnyy Vladimir Aladinskiy Daniil Polykovskiy Evgeny Putin Petrina Kamya Alexander Aliper Alex Zhavoronkov Chemistry42: An AI-based platform for de novo molecular design. 2021 abs/2101.09050 CoRR https://arxiv.org/abs/2101.09050 db/journals/corr/corr2101.html#abs-2101-09050

Alexey A. Moskalev Svetlana Zhikrivetskaya Mikhail Shaposhnikov Evgenia Dobrovolskaya Roman Gurinovich Oleg Kuryan Aleksandr Pashuk Leslie C. Jellen Alex Aliper Alex Peregudov Alex Zhavoronkov Aging Chart: a community resource for rapid exploratory pathway analysis of age-related processes. 894-899 2016 44 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkv1287 https://www.wikidata.org/entity/Q28603043 db/journals/nar/nar44.html#MoskalevZSDGKPJ16

Nishant Agrawal Vladimir Aladinskiy Alexander Amini Alán Aspuru-Guzik Eugene Babin Mihir Bafna Dmitry Bezrukov Lela Bitar Nikita Bondarev Annika Brundyn Xin Cai Yudong Cao Zhongying Cao Shan Chen Wei-Yin Chiang Stephanie M. Cope Anthony Costa Krishna M. Padmanabha Das Xiao Ding Xiaoyu Ding Evgenia Dobrovolskaya Alexey Dubovenko Tatyana Fokina Egor Galkin Fedor Galkin Mohammad GhazivakiliMohammad Ghazi Vakili Christoph Gorgulla Roman Gurinovich Ramin M. Hasani Jen-Yueh Hsiao Min-Hsiu Hsieh Ivan Ilin Yan IvanenkovYan A. Ivanenkov Evgeny Izumchenko Leslie C. Jellen Aastha Jhunjhunwala Alexander A. Kalashnikov Petrina Kamya Po-Yu Kao Kaeli Kaymak-Loveless Shanshan Kong Mikhail Korzinkin Ekaterina Kozlova Oleg Kuryan Maksim Kuznetsov Mathias Lechner Michael Levitt 0001 Arkadii Lin Sha Lin Yen-Chu Lin Bonnie Hei Man Liu Jinxin Liu Yingtao Liu Micha Livne Xi Long Anna Lyakisheva Thomas MacDougall Maxim Malkov Ardalan Hosseini Mansob Alexey Mantsyzov Elizabeth McMichael Fanye Meng Zulfat Miftahutdinov Zulfat Miftakhutdinov Mikolaj Mizera Anton Morgunov Alexey A. Moskalev Vladimir Naumov AkshatKumar Nigam Tudor I. Oprea Ivan OzerovIvan V. Ozerov Aleksandr Pashuk Alexander T. Pearson Alex Peregudov Daniil Polykovskiy Frank W. Pun Stefan Pushkov Evgeny Putin Eugene Radchenko Feng Ren Mathieu Reymond Konstantin Romantsov Fedor Ryabov Roman Schutski Ramanathan Sethuraman Mikhail Shaposhnikov Rim Shayakhmetov Anastasia Shneyderman Jamie Snider Igor Stagljar Savas Tay Nina Tihonova Kyle Tretina Elena Tutubalina Airat Valiev Quentin Vanhaelen Daniel Varoli Ju Wang Tianbiao Yang Ya-Chu Yang Zhong Yao Bogdan Zagribelnyy Alex Zhavoronkov Alexander Zhebrak Min Zheng Svetlana Zhikrivetskaya Wei Zhu Arsenii Zinkevich