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Generative models hold great promise for small molecule discovery, significantly increasing the size of search space compared to traditional in silico screening libraries.
Uff, a full periodic table force field for molecular mechanics and molecular dynamics simulations
A. K. Rappe, C. J. Casewit, K. S. Colwell, W. A. III Goddard, and W. M. Skiff · 1992
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Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
Christopher A Lipinski, Franco Lombardo, Beryl W Dominy, and Paul J Feeney · 1997
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TBLR1 regulates the expression of nuclear hormone receptor co-repressors
Xin-Min Zhang, Qing Chang, Lin Zeng, Judy Gu, Stuart Brown, and Ross S Basch · 2006
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Unbiasing scoring functions: a new normalization and rescoring strategy
Giorgio Carta, Andrew JS Knox, and David G Lloyd · 2007
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Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions
Peter Ertl and Ansgar Schuffenhauer · 2009
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Molecular shape and medicinal chemistry: A perspective
Anthony Nicholls, Georgia B. McGaughey, Robert P. Sheridan, Andrew C. Good, Gregory Warren, Magali Mathieu, Steven W. Muchmore, Scott P. Brown, J. Andrew Grant, James A. Haigh, Neysa Nevins, Ajay N. Jain, and Brian Kelley · 2010
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Boronic acids in medicinal chemistry: anticancer, antibacterial and antiviral applications
Paul C. Trippier and Christopher McGuigan · 2010
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AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott and Arthur J Olson · 2010
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Extraction of chemical structures and reactions from the literature
Daniel Mark Lowe · 2012
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Design and discovery of soluble epoxide hydrolase inhibitors for the treatment of cardiovascular diseases
Thomas Duflot, Clothilde Roche, Fabien Lamoureux, Dominique Guerrot, and Jeremy Bellien · 2014
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Extensive consensus docking evaluation for ligand pose prediction and virtual screening studies
Tiziano Tuccinardi, Giulio Poli, Veronica Romboli, Antonio Giordano, and Adriano Martinelli · 2014
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Fast, accurate, and reliable molecular docking with QuickVina 2
Amr Alhossary, Stephanus Daniel Handoko, Yuguang Mu, and Chee-Keong Kwoh · 2015
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An aggregation advisor for ligand discovery
John J. Irwin, Da Duan, Hayarpi Torosyan, Allison K. Doak, Kristin T. Ziebart, Teague Sterling, Gurgen Tumanian, and Brian K. Shoichet · 2015
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Better informed distance geometry: Using what we know to improve conformation generation
Sereina Riniker and Gregory A. Landrum · 2015
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ZINC 15–ligand discovery for everyone
Teague Sterling and John J Irwin · 2015
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Analysis of past and present synthetic methodologies on medicinal chemistry: Where have all the new reactions gone? Miniperspective
Dean G. Brown and Jonas Boström · 2016
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Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power
Zhe Wang, Huiyong Sun, Xiaojun Yao, Dan Li, Lei Xu, Youyong Li, Sheng Tian, and Tingjun Hou · 2016
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Molecular de-novo design through deep reinforcement learning
Marcus Olivecrona, Thomas Blaschke, Ola Engkvist, and Hongming Chen · 2017
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MeCP2 mutations: progress towards understanding and treating rett syndrome
Ruth R Shah and Adrian P Bird · 2017
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The role of ClpP protease in bacterial pathogenesis and human diseases
Vaibhav Bhandari, Keith S Wong, Jin Lin Zhou, Mark F Mabanglo, Robert A Batey, and Walid A Houry · 2018
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Junction tree variational autoencoder for molecular graph generation
Wengong Jin, Regina Barzilay, and Tommi Jaakkola · 2018
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Conditional molecular design with deep generative models
Seokho Kang and Kyunghyun Cho · 2018
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A model to search for synthesizable molecules
John Bradshaw, Brooks Paige, Matt J Kusner, Marwin Segler, and José Miguel Hernández-Lobato · 2019
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GuacaMol: benchmarking models for de novo molecular design
Nathan Brown, Marco Fiscato, Marwin HS Segler, and Alain C Vaucher · 2019
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Automated de novo molecular design by hybrid machine intelligence and rule-driven chemical synthesis
Alexander Button, Daniel Merk, Jan A Hiss, and Gisbert Schneider · 2019
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Mitochondrial protease ClpP is a target for the anticancer compounds ONC201 and related analogues
Paul R Graves, Lucas J Aponte-Collazo, Emily M J Fennell, Adam C Graves, Andrew E Hale, Nedyalka Dicheva, Laura E Herring, Thomas S K Gilbert, Michael P East, Ian M McDonald, Matthew R Lockett, Hani Ashamalla, Nathaniel J Moorman, Donald S Karanewsky, Edwin J Iwanowicz, Ekhson Holmuhamedov, and Lee M Graves · 2019
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Mitochondrial ClpP-mediated proteolysis induces selective cancer cell lethality
Jo Ishizawa, Sarah F Zarabi, R Eric Davis, Ondrej Halgas, Takenobu Nii, Yulia Jitkova, Ran Zhao, Jonathan St-Germain, Lauren E Heese, Grace Egan, Vivian R Ruvolo, Samir H Barghout, Yuki Nishida, Rose Hurren, Wencai Ma, Marcela Gronda, Todd Link, Keith Wong, Mark Mabanglo, Kensuke Kojima, Gautam Borthakur, Neil MacLean, Man Chun John Ma, Andrew B Leber, Mark D Minden, Walid Houry, Hagop Kantarjian, Martin Stogniew, Brian Raught, Emil F Pai, Aaron D Schimmer, and Michael Andreeff · 2019
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A graph-based genetic algorithm and generative model/Monte Carlo tree search for the exploration of chemical space
Jan H Jensen · 2019
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Ultra-large library docking for discovering new chemotypes
Jiankun Lyu, Sheng Wang, Trent E. Balius, Isha Singh, Anat Levit, Yurii S. Moroz, Matthew J. O’Meara, Tao Che, Enkhjargal Algaa, Kateryna Tolmachova, Andrey A. Tolmachev, Brian K. Shoichet, Bryan L. Roth, and John J. Irwin · 2019
Cited alongside, same era.
Graph transformer networks
Seongjun Yun, Minbyul Jeong, Raehyun Kim, Jaewoo Kang, and Hyunwoo J Kim · 2019
Cited alongside, same era.
SMILES-based deep generative scaffold decorator for de-novo drug design
Generating reaction trees with cascaded variational autoencoders
Dai Hai Nguyen and Koji Tsuda · 2022
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Evaluating generalization in GFlowNets for molecule design
Andrei Cristian Nica, Moksh Jain, Emmanuel Bengio, Cheng-Hao Liu, Maksym Korablyov, Michael M Bronstein, and Yoshua Bengio · 2022
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An efficient graph generative model for navigating ultra-large combinatorial synthesis libraries
Aryan Pedawi, Pawel Gniewek, Chaoyi Chang, Brandon Anderson, and Henry van den Bedem · 2022
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Synthon-based ligand discovery in virtual libraries of over 11 billion compounds
Arman A. Sadybekov, Anastasiia V. Sadybekov, Yongfeng Liu, Christos Iliopoulos-Tsoutsouvas, Xi-Ping Huang, Julie Pickett, Blake Houser, Nilkanth Patel, Ngan K. Tran, Fei Tong, Nikolai Zvonok, Manish K. Jain, Olena Savych, Dmytro S. Radchenko, Spyros P. Nikas, Nicos A. Petasis, Yurii S. Moroz, Bryan L. Roth, Alexandros Makriyannis, and Vsevolod Katritch · 2022
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A screen for MeCP2-TBL1 interaction inhibitors using a luminescence-based assay
Beatrice Alexander-Howden, Li Zhang, Almer M van der Sloot, Sylvain Tollis, Daniel J St-Cyr, Frank Sicheri, Adrian P Bird, Mike Tyers, and Matthew J Lyst · 2023
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Josep Arús-Pous, Atanas Patronov, Esben Jannik Bjerrum, Christian Tyrchan, Jean-Louis Reymond, Hongming Chen, and Ola Engkvist · 2020
Cited alongside, same era.
Open science discovery of potent non-covalent SARS-CoV-2 main protease inhibitors
COVID Moonshot Consortium, Hagit Achdout, Anthony Aimon, Dominic S Alonzi, Robert Arbon, Elad Bar-David, Haim Barr, Amir Ben-Shmuel, James Bennett, Vitaliy A Bilenko, et al · 2020
Cited alongside, same era.
The synthesizability of molecules proposed by generative models
Wenhao Gao and Connor W Coley · 2020
Cited alongside, same era.
AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning
Samuel Genheden, Amol Thakkar, Veronika Chadimová, Jean-Louis Reymond, Ola Engkvist, and Esben Bjerrum · 2020
Cited alongside, same era.
Learning to navigate the synthetically accessible chemical space using reinforcement learning
Sai Krishna Gottipati, Boris Sattarov, Sufeng Niu, Yashaswi Pathak, Haoran Wei, Shengchao Liu, Simon Blackburn, Karam Thomas, Connor Coley, Jian Tang, et al · 2020
Cited alongside, same era.
Molecular design in synthetically accessible chemical space via deep reinforcement learning
Julien Horwood and Emmanuel Noutahi · 2020
Cited alongside, same era.
Imipridone anticancer compounds ectopically activate the ClpP protease and represent a new scaffold for antibiotic development
Samuel Jacques, Almer M van der Sloot, Caroline C Huard, Jasmin Coulombe-Huntington, Sarah Tsao, Sylvain Tollis, Thierry Bertomeu, Elizabeth J Culp, Daniel Pallant, Michael A Cook, Eric Bonneil, Pierre Thibault, Gerard D Wright, and Mike Tyers · 2020
Cited alongside, same era.
Structural plasticity of SARS-CoV-2 3CL mpro active site cavity revealed by room temperature x-ray crystallography
Daniel W Kneller, Gwyndalyn Phillips, Hugh M O’Neill, Robert Jedrzejczak, Lucy Stols, Paul Langan, Andrzej Joachimiak, Leighton Coates, and Andrey Kovalevsky · 2020
Cited alongside, same era.
Later among the works it cites.
GFlowNet foundations
Yoshua Bengio, Salem Lahlou, Tristan Deleu, Edward J Hu, Mo Tiwari, and Emmanuel Bengio · 2023
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PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences, 2023
Martin Buttenschoen, Garrett M. Morris, and Charlotte M. Deane · 2023
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Multi-fidelity active learning with GFlowNets
Alex Hernandez-Garcia, Nikita Saxena, Moksh Jain, Cheng-Hao Liu, and Yoshua Bengio · 2023
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Bridging the gap between chemical reaction pretraining and conditional molecule generation with a unified model
Bo Qiang, Yiran Zhou, Yuheng Ding, Ningfeng Liu, Song Song, Liangren Zhang, Bo Huang, and Zhenming Liu · 2023
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Goal-conditioned GFlowNets for controllable multi-objective molecular design
Julien Roy, Pierre-Luc Bacon, Christopher Pal, and Emmanuel Bengio · 2023
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SILVR: Guided diffusion for molecule generation
Nicholas T Runcie and Antonia SJS Mey · 2023
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TacoGFN: Target conditioned gflownet for structure-based drug design
Tony Shen, Mohit Pandey, and Martin Ester · 2023
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Discovery of senolytics using machine learning
Vanessa Smer-Barreto, Andrea Quintanilla, Richard JR Elliott, John C Dawson, Jiugeng Sun, Víctor M Campa, Álvaro Lorente-Macías, Asier Unciti-Broceta, Neil O Carragher, Juan Carlos Acosta, et al · 2023
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Vina-GPU 2.1: towards further optimizing docking speed and precision of AutoDock Vina and its derivatives
Shidi Tang, Ji Ding, Xiangyu Zhu, Zheng Wang, Haitao Zhao, and Jiansheng Wu · 2023
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Discovering small-molecule senolytics with deep neural networks
Felix Wong, Satotaka Omori, Nina M Donghia, Erica J Zheng, and James J Collins · 2023
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SynFlowNet: Towards molecule design with guaranteed synthesis pathways
Miruna Cretu, Charles Harris, Julien Roy, Emmanuel Bengio, and Pietro Lio · 2024
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Enamine REAL database
Enamine · 2024
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RetroGFN: Diverse and feasible retrosynthesis using GFlowNets
Piotr Gaiński, Michał Koziarski, Krzysztof Maziarz, Marwin Segler, Jacek Tabor, and Marek Śmieja · 2024
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Generative active learning for the search of small-molecule protein binders
Maksym Korablyov, Cheng-Hao Liu, Moksh Jain, Almer M van der Sloot, Eric Jolicoeur, Edward Ruediger, Andrei Cristian Nica, Emmanuel Bengio, Kostiantyn Lapchevskyi, Daniel St-Cyr, et al · 2024
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3D molecule generation by denoising voxel grids
Pedro O O Pinheiro, Joshua Rackers, Joseph Kleinhenz, Michael Maser, Omar Mahmood, Andrew Watkins, Stephen Ra, Vishnu Sresht, and Saeed Saremi · 2024
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Recursion GFlowNet repository
Recursion · 2024
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A high-throughput phenotypic screen combined with an ultra-large-scale deep learning-based virtual screening reveals novel scaffolds of antibacterial compounds
Gabriele Scalia, Steven T Rutherford, Ziqing Lu, Kerry R Buchholz, Nicholas Skelton, Kangway Chuang, Nathaniel Diamant, Jan-Christian Huetter, Jerome Luescher, Ahn Miu, et al · 2024
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Generative AI for designing and validating easily synthesizable and structurally novel antibiotics
Kyle Swanson, Gary Liu, Denise B Catacutan, Autumn Arnold, James Zou, and Jonathan M Stokes · 2024
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Towards equilibrium molecular conformation generation with GFlowNets
Alexandra Volokhova, Michał Koziarski, Alex Hernández-García, Cheng-Hao Liu, Santiago Miret, Pablo Lemos, Luca Thiede, Zichao Yan, Alán Aspuru-Guzik, and Yoshua Bengio · 2024
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Diversity-oriented synthesis as a tool for the discovery of novel biologically active small molecules
Warren R.J.D. Galloway, Albert Isidro-Llobet, and David R. Spring · 2041
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