Fetching the paper…
Reading the bibliography…
Structure-based drug design (SBDD) aims to generate ligands that bind strongly and specifically to target protein pockets.
Structure-based drug design
Tom L Blundell · 1996
Earlier work this paper cites.
The process of structure-based drug design
Amy C Anderson · 2003
Earlier work this paper cites.
Glide: a new approach for rapid, accurate docking and scoring. 2. enrichment factors in database screening
Thomas A Halgren, Robert B Murphy, Richard A Friesner, Hege S Beard, Leah L Frye, W Thomas Pollard, and Jay L Banks · 2004
Earlier work this paper cites.
The pdbbind database: methodologies and updates
Renxiao Wang, Xueliang Fang, Yipin Lu, Chao-Yie Yang, and Shaomeng Wang · 2005
Earlier work this paper cites.
Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions
Peter Ertl and Ansgar Schuffenhauer · 2009
Earlier work this paper cites.
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
Earlier work this paper cites.
Quantifying the chemical beauty of drugs
G Richard Bickerton, Gaia V Paolini, Jérémy Besnard, Sorel Muresan, and Andrew L Hopkins · 2012
Earlier work this paper cites.
Adam: A method for stochastic optimization
P Kingma Diederik · 2014
Earlier work this paper cites.
Fast, accurate, and reliable molecular docking with quickvina 2
Amr Alhossary, Stephanus Daniel Handoko, Yuguang Mu, and Chee-Keong Kwoh · 2015
Earlier work this paper cites.
Generative modeling by estimating gradients of the data distribution
Yang Song and Stefano Ermon · 2019
Earlier work this paper cites.
Comparative assessment of scoring functions: The casf-2016 update
Minyi Su, Qifan Yang, Yu Du, Guoqin Feng, Zhihai Liu, Yan Li, and Renxiao Wang · 2019
Earlier work this paper cites.
The synthesizability of molecules proposed by generative models
Wenhao Gao and Connor W. Coley · 2020
Cited alongside, same era.
Score-based generative modeling through stochastic differential equations
Yang Song, Jascha Sohl-Dickstein, Diederik P Kingma, Abhishek Kumar, Stefano Ermon, and Ben Poole · 2020
Cited alongside, same era.
Three-dimensional convolutional neural networks and a cross-docked data set for structure-based drug design
Paul G Francoeur, Tomohide Masuda, Jocelyn Sunseri, Andrew Jia, Richard B Iovanisci, Ian Snyder, and David R Koes · 2020
Cited alongside, same era.
Denoising diffusion probabilistic models
Jonathan Ho, Ajay Jain, and Pieter Abbeel · 2020
Cited alongside, same era.
Diffusion models beat gans on image synthesis
Prafulla Dhariwal and Alexander Nichol · 2021
Cited alongside, same era.
Pocket2mol: Efficient molecular sampling based on 3d protein pockets
Xingang Peng, Shitong Luo, Jiaqi Guan, Qi Xie, Jian Peng, and Jianzhu Ma · 2022
Later among the works it cites.
Generating 3d molecules for target protein binding
Meng Liu, Youzhi Luo, Kanji Uchino, Koji Maruhashi, and Shuiwang Ji · 2022
Later among the works it cites.
Generating 3d molecules conditional on receptor binding sites with deep generative models
Matthew Ragoza, Tomohide Masuda, and David Ryan Koes · 2022
Later among the works it cites.
Benchmarking generated poses: How rational is structure-based drug design with generative models?
Charles Harris, Kieran Didi, Arian R Jamasb, Chaitanya K Joshi, Simon V Mathis, Pietro Lio, and Tom Blundell · 2023
Later among the works it cites.
Coarsenconf: Equivariant coarsening with aggregated attention for molecular conformer generation
Danny Reidenbach and Aditi S Krishnapriyan · 2024
alphaXiv searches the wider corpus for related work and actual follow-ups.
alphaXiv is searching for related work…
Shitong Luo, Jiaqi Guan, Jianzhu Ma, and Jian Peng · 2021
Cited alongside, same era.
E (n) equivariant graph neural networks
Vıctor Garcia Satorras, Emiel Hoogeboom, and Max Welling · 2021
Cited alongside, same era.
Geodiff: A geometric diffusion model for molecular conformation generation
Minkai Xu, Lantao Yu, Yang Song, Chence Shi, Stefano Ermon, and Jian Tang · 2022
Cited alongside, same era.
Equivariant diffusion for molecule generation in 3d
Emiel Hoogeboom, Vıctor Garcia Satorras, Clément Vignac, and Max Welling · 2022
Cited alongside, same era.
Structure-based drug design with equivariant diffusion models
Arne Schneuing, Yuanqi Du, Charles Harris, Arian Jamasb, Ilia Igashov, Weitao Du, Tom Blundell, Pietro Lió, Carla Gomes, Max Welling, et al · 2022
Cited alongside, same era.
3d equivariant diffusion for target-aware molecule generation and affinity prediction
Jiaqi Guan, Wesley Wei Qian, Xingang Peng, Yufeng Su, Jian Peng, and Jianzhu Ma
Cited in the paper.
Decompdiff: diffusion models with decomposed priors for structure-based drug design
Jiaqi Guan, Xiangxin Zhou, Yuwei Yang, Yu Bao, Jian Peng, Jianzhu Ma, Qiang Liu, Liang Wang, and Quanquan Gu
Cited in the paper.
Closest in time.
Evosbdd: Latent evolution for accurate and efficient structure-based drug design
Danny Reidenbach · 2024
Closest in time.
Rethinking specificity in sbdd: Leveraging delta score and energy-guided diffusion
Bowen Gao, Minsi Ren, Yuyan Ni, Yanwen Huang, Bo Qiang, Zhi-Ming Ma, Wei-Ying Ma, and Yanyan Lan · 2024
Closest in time.
Structure-based drug design with equivariant diffusion models
Arne Schneuing, Charles Harris, Yuanqi Du, Kieran Didi, Arian Jamasb, Ilia Igashov, Weitao Du, Carla Gomes, Tom L Blundell, Pietro Lio, et al · 2024
Closest in time.
Equivariant 3d-conditional diffusion model for molecular linker design
Ilia Igashov, Hannes Stärk, Clément Vignac, Arne Schneuing, Victor Garcia Satorras, Pascal Frossard, Max Welling, Michael Bronstein, and Bruno Correia · 2024
Closest in time.
Action-minimization meets generative modeling: Efficient transition path sampling with the onsager-machlup functional
Sanjeev Raja, Martin Sipka, Michael Psenka, Tobias Kreiman, Michal Pavelka, and Aditi S. Krishnapriyan · 2025
Closest in time.