From target to drug: generative modeling for the multimodal structure-based ligand design

M Skalic, D Sabbadin, B Sattarov… - Molecular …, 2019 - ACS Publications
Chemical space is impractically large, and conventional structure-based virtual screening
techniques cannot be used to simply search through the entire space to discover effective …

OptiMol: Optimization of Binding Affinities in Chemical Space for Drug Discovery

J Boitreaud, V Mallet, C Oliver… - Journal of Chemical …, 2020 - ACS Publications
Ligand-based drug design has recently benefited from the development of deep generative
models. These models enable extensive explorations of the chemical space and provide a …

Deep generative design with 3D pharmacophoric constraints

F Imrie, TE Hadfield, AR Bradley, CM Deane - Chemical science, 2021 - pubs.rsc.org
Generative models have increasingly been proposed as a solution to the molecular design
problem. However, it has proved challenging to control the design process or incorporate …

Relation: A deep generative model for structure-based de novo drug design

M Wang, CY Hsieh, J Wang, D Wang… - Journal of Medicinal …, 2022 - ACS Publications
Deep learning (DL)-based de novo molecular design has recently gained considerable
traction. Many DL-based generative models have been successfully developed to design …

Computational approaches streamlining drug discovery

AV Sadybekov, V Katritch - Nature, 2023 - nature.com
Computer-aided drug discovery has been around for decades, although the past few years
have seen a tectonic shift towards embracing computational technologies in both academia …

Deep generative models for 3D linker design

F Imrie, AR Bradley, M van der Schaar… - Journal of chemical …, 2020 - ACS Publications
Rational compound design remains a challenging problem for both computational methods
and medicinal chemists. Computational generative methods have begun to show promising …

3D molecular generative framework for interaction-guided drug design

W Zhung, H Kim, WY Kim - Nature Communications, 2024 - nature.com
Deep generative modeling has a strong potential to accelerate drug design. However,
existing generative models often face challenges in generalization due to limited data …

A pocket-based 3D molecule generative model fueled by experimental electron density

L Wang, R Bai, X Shi, W Zhang, Y Cui, X Wang… - Scientific reports, 2022 - nature.com
We report for the first time the use of experimental electron density (ED) as training data for
the generation of drug-like three-dimensional molecules based on the structure of a target …

DecompDiff: diffusion models with decomposed priors for structure-based drug design

J Guan, X Zhou, Y Yang, Y Bao, J Peng, J Ma… - arXiv preprint arXiv …, 2024 - arxiv.org
Designing 3D ligands within a target binding site is a fundamental task in drug discovery.
Existing structured-based drug design methods treat all ligand atoms equally, which ignores …

A 3D generative model for structure-based drug design

S Luo, J Guan, J Ma, J Peng - Advances in Neural …, 2021 - proceedings.neurips.cc
We study a fundamental problem in structure-based drug design---generating molecules
that bind to specific protein binding sites. While we have witnessed the great success of …