Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning

A Kroll, Y Rousset, XP Hu, NA Liebrand… - Nature …, 2023 - nature.com
The turnover number k cat, a measure of enzyme efficiency, is central to understanding
cellular physiology and resource allocation. As experimental k cat estimates are unavailable …

Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Sco** 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 …

Symmetry-informed geometric representation for molecules, proteins, and crystalline materials

S Liu, Y Li, Z Li, Z Zheng, C Duan… - Advances in neural …, 2023 - proceedings.neurips.cc
Artificial intelligence for scientific discovery has recently generated significant interest within
the machine learning and scientific communities, particularly in the domains of chemistry …

Artificial intelligence in synthetic chemistry: achievements and prospects

II Baskin, TI Madzhidov, IS Antipin… - Russian Chemical …, 2017 - iopscience.iop.org
The review is devoted to the achievements in analysis of information on chemical reactions
using machine learning methods. Four large areas that actively use these methods are …

ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature

A Dalkiran, AS Rifaioglu, MJ Martin, R Cetin-Atalay… - BMC …, 2018 - Springer
Background The automated prediction of the enzymatic functions of uncharacterized
proteins is a crucial topic in bioinformatics. Although several methods and tools have been …

Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

MA Campodonico, BA Andrews, JA Asenjo… - Metabolic …, 2014 - Elsevier
The production of 75% of the current drug molecules and 35% of all chemicals could be
achieved through bioprocessing (Arundel and Sawaya, 2009). To accelerate the transition …

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites

N Hadadi, H MohammadiPeyhani, L Miskovic… - Proceedings of the …, 2019 - pnas.org
Thousands of biochemical reactions with characterized activities are “orphan,” meaning they
cannot be assigned to a specific enzyme, leaving gaps in metabolic pathways. Novel …

Development and application of a data-driven reaction classification model: comparison of an electronic lab notebook and medicinal chemistry literature

GM Ghiandoni, MJ Bodkin, B Chen… - Journal of chemical …, 2019 - ACS Publications
Reaction classification has often been considered an important task for many different
applications, and has traditionally been accomplished using hand-coded rule-based …

Methylglucosylation of aromatic amino and phenolic moieties of drug-like biosynthons by combinatorial biosynthesis

L **e, L Zhang, C Wang, X Wang, Y Xu, H Yu… - Proceedings of the …, 2018 - pnas.org
Glycosylation is a prominent strategy to optimize the pharmacokinetic and
pharmacodynamic properties of drug-like small-molecule scaffolds by modulating their …

A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks

H Nam, M Campodonico, A Bordbar… - PLoS computational …, 2014 - journals.plos.org
Altered metabolism in cancer cells has been viewed as a passive response required for a
malignant transformation. However, this view has changed through the recently described …