Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Scoping Review

G Gricourt, P Meyer, T Duigou, JL Faulon - ACS Synthetic Biology, 2024 - ACS Publications
Retrosynthesis aims to efficiently plan the synthesis of desirable chemicals by strategically
breaking down molecules into readily available building block compounds. Having a long …

Retro-fallback: retrosynthetic planning in an uncertain world

A Tripp, K Maziarz, S Lewis, M Segler… - arXiv preprint arXiv …, 2023 - arxiv.org
Retrosynthesis is the task of proposing a series of chemical reactions to create a desired
molecule from simpler, buyable molecules. While previous works have proposed algorithms …

A unified view of deep learning for reaction and retrosynthesis prediction: current status and future challenges

Z Meng, P Zhao, Y Yu, I King - arXiv preprint arXiv:2306.15890, 2023 - arxiv.org
Reaction and retrosynthesis prediction are fundamental tasks in computational chemistry
that have recently garnered attention from both the machine learning and drug discovery …

READRetro: natural product biosynthesis predicting with retrieval‐augmented dual‐view retrosynthesis

T Kim, S Lee, Y Kwak, MS Choi, J Park… - New …, 2024 - Wiley Online Library
Plants, as a sessile organism, produce various secondary metabolites to interact with the
environment. These chemicals have fascinated the plant science community because of …

Globally Interpretable Graph Learning via Distribution Matching

Y Nian, Y Chang, W Jin, L Lin - Proceedings of the ACM on Web …, 2024 - dl.acm.org
Graph neural networks (GNNs) have emerged as a powerful model to capture critical graph
patterns. Instead of treating them as black boxes in an end-to-end fashion, attempts are …

MARS: a motif-based autoregressive model for retrosynthesis prediction

J Liu, C Yan, Y Yu, C Lu, J Huang, L Ou-Yang… - …, 2024 - academic.oup.com
Motivation Retrosynthesis is a critical task in drug discovery, aimed at finding a viable
pathway for synthesizing a given target molecule. Many existing approaches frame this task …

Neural Atoms: Propagating Long-range Interaction in Molecular Graphs through Efficient Communication Channel

X Li, Z Zhou, J Yao, Y Rong, L Zhang… - The Twelfth International …, 2024 - openreview.net
Graph Neural Networks (GNNs) have been widely adopted for drug discovery with
molecular graphs. Nevertheless, current GNNs mainly excel in leveraging short-range …

RetroCaptioner: beyond attention in end-to-end retrosynthesis transformer via contrastively captioned learnable graph representation

X Liu, C Ai, H Yang, R Dong, J Tang, S Zheng… - …, 2024 - academic.oup.com
Motivation Retrosynthesis identifies available precursor molecules for various and novel
compounds. With the advancements and practicality of language models, Transformer …

Preference Optimization for Molecule Synthesis with Conditional Residual Energy-based Models

S Liu, H Dai, Y Zhao, P Liu - arXiv preprint arXiv:2406.02066, 2024 - arxiv.org
Molecule synthesis through machine learning is one of the fundamental problems in drug
discovery. Current data-driven strategies employ one-step retrosynthesis models and search …

ASKCOS: an open source software suite for synthesis planning

Z Tu, SJ Choure, MH Fong, J Roh, I Levin, K Yu… - arXiv preprint arXiv …, 2025 - arxiv.org
The advancement of machine learning and the availability of large-scale reaction datasets
have accelerated the development of data-driven models for computer-aided synthesis …