Generative models as an emerging paradigm in the chemical sciences

DM Anstine, O Isayev - Journal of the American Chemical Society, 2023 - ACS Publications
Traditional computational approaches to design chemical species are limited by the need to
compute properties for a vast number of candidates, eg, by discriminative modeling …

[HTML][HTML] De novo molecular design and generative models

J Meyers, B Fabian, N Brown - Drug discovery today, 2021 - Elsevier
Molecular design strategies are integral to therapeutic progress in drug discovery.
Computational approaches for de novo molecular design have been developed over the …

Docking-based generative approaches in the search for new drug candidates

T Danel, J Łęski, S Podlewska, IT Podolak - Drug Discovery Today, 2023 - Elsevier
Highlights•Compound enumeration coupled with docking is rapidly gaining
popularity.•Docking-based generative models are reviewed.•New taxonomy for docking …

Tartarus: A benchmarking platform for realistic and practical inverse molecular design

AK Nigam, R Pollice, G Tom, K Jorner… - Advances in …, 2023 - proceedings.neurips.cc
The efficient exploration of chemical space to design molecules with intended properties
enables the accelerated discovery of drugs, materials, and catalysts, and is one of the most …

Artificial intelligence and cheminformatics tools: a contribution to the drug development and chemical science

I Saifi, BA Bhat, SS Hamdani, UY Bhat… - Journal of …, 2024 - Taylor & Francis
In the ever-evolving field of drug discovery, the integration of Artificial Intelligence (AI) and
Machine Learning (ML) with cheminformatics has proven to be a powerful combination …

Parallel tempered genetic algorithm guided by deep neural networks for inverse molecular design

AK Nigam, R Pollice, A Aspuru-Guzik - Digital Discovery, 2022 - pubs.rsc.org
Inverse molecular design involves algorithms that sample molecules with specific target
properties from a multitude of candidates and can be posed as an optimization problem …

Reconstruction of lossless molecular representations from fingerprints

UV Ucak, I Ashyrmamatov, J Lee - Journal of cheminformatics, 2023 - Springer
The simplified molecular-input line-entry system (SMILES) is the most prevalent molecular
representation used in AI-based chemical applications. However, there are innate limitations …

ChemistGA: a chemical synthesizable accessible molecular generation algorithm for real-world drug discovery

J Wang, X Wang, H Sun, M Wang, Y Zeng… - Journal of Medicinal …, 2022 - ACS Publications
Many deep learning (DL)-based molecular generative models have been proposed to
design novel molecules. These models may perform well on benchmarks, but they usually …

JANUS: parallel tempered genetic algorithm guided by deep neural networks for inverse molecular design

AK Nigam, R Pollice, A Aspuru-Guzik - arxiv preprint arxiv:2106.04011, 2021 - arxiv.org
Inverse molecular design, ie, designing molecules with specific target properties, can be
posed as an optimization problem. High-dimensional optimization tasks in the natural …

Local scaffold diversity-contributed generator for discovering potential NLRP3 inhibitors

W Bo, Y Duan, Y Zou, Z Ma, T Yang… - Journal of Chemical …, 2024 - ACS Publications
Deep generative models have become crucial tools in de novo drug design. In current
models for multiobjective optimization in molecular generation, the scaffold diversity is …