OpenChem: a deep learning toolkit for computational chemistry and drug design

M Korshunova, B Ginsburg, A Tropsha… - Journal of Chemical …, 2021 - ACS Publications
Deep learning models have demonstrated outstanding results in many data-rich areas of
research, such as computer vision and natural language processing. Currently, there is a …

De Novo Structure-Based Drug Design Using Deep Learning

SR Krishnan, N Bung, SR Vangala… - Journal of chemical …, 2021 - ACS Publications
In recent years, deep learning-based methods have emerged as promising tools for de novo
drug design. Most of these methods are ligand-based, where an initial target-specific ligand …

Analyzing learned molecular representations for property prediction

K Yang, K Swanson, W Jin, C Coley… - Journal of chemical …, 2019 - ACS Publications
Advancements in neural machinery have led to a wide range of algorithmic solutions for
molecular property prediction. Two classes of models in particular have yielded promising …

Transformer-based molecular optimization beyond matched molecular pairs

J He, E Nittinger, C Tyrchan, W Czechtizky… - Journal of …, 2022 - Springer
Molecular optimization aims to improve the drug profile of a starting molecule. It is a
fundamental problem in drug discovery but challenging due to (i) the requirement of …

Augmenting genetic algorithms with deep neural networks for exploring the chemical space

AK Nigam, P Friederich, M Krenn… - arXiv preprint arXiv …, 2019 - arxiv.org
Challenges in natural sciences can often be phrased as optimization problems. Machine
learning techniques have recently been applied to solve such problems. One example in …

[HTML][HTML] On failure modes in molecule generation and optimization

P Renz, D Van Rompaey, JK Wegner… - Drug Discovery Today …, 2019 - Elsevier
There has been a wave of generative models for molecules triggered by advances in the
field of Deep Learning. These generative models are often used to optimize chemical …

Recent applications of machine learning in medicinal chemistry

J Panteleev, H Gao, L Jia - Bioorganic & medicinal chemistry letters, 2018 - Elsevier
In recent decades, artificial intelligence and machine learning have played a significant role
in increasing the efficiency of processes across a wide spectrum of industries. When it …

A perspective on deep learning for molecular modeling and simulations

J Zhang, YK Lei, Z Zhang, J Chang, M Li… - The Journal of …, 2020 - ACS Publications
Deep learning is transforming many areas in science, and it has great potential in modeling
molecular systems. However, unlike the mature deployment of deep learning in computer …

Optimization‐based framework for computer‐aided molecular design

AP Samudra, NV Sahinidis - AIChE Journal, 2013 - Wiley Online Library
A new framework to automate, augment, and accelerate steps in computer‐aided molecular
design is presented. The problem is tackled in three stages:(1) composition design,(2) …

[HTML][HTML] Quantum computing for chemical and biomolecular product design

MP Andersson, MN Jones, KV Mikkelsen, F You… - Current Opinion in …, 2022 - Elsevier
Highlights•Quantum computing and its use for computer-aided product design is discussed
and perspectives for several types of problems are provided.•Hybrid QC methods are likely …