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Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning
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 …
cellular physiology and resource allocation. As experimental k cat estimates are unavailable …
Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Sco** Review
Retrosynthesis aims to efficiently plan the synthesis of desirable chemicals by strategically
breaking down molecules into readily available building block compounds. Having a long …
breaking down molecules into readily available building block compounds. Having a long …
Symmetry-informed geometric representation for molecules, proteins, and crystalline materials
Artificial intelligence for scientific discovery has recently generated significant interest within
the machine learning and scientific communities, particularly in the domains of chemistry …
the machine learning and scientific communities, particularly in the domains of chemistry …
Artificial intelligence in synthetic chemistry: achievements and prospects
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 …
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
Background The automated prediction of the enzymatic functions of uncharacterized
proteins is a crucial topic in bioinformatics. Although several methods and tools have been …
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 …
achieved through bioprocessing (Arundel and Sawaya, 2009). To accelerate the transition …
Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites
Thousands of biochemical reactions with characterized activities are “orphan,” meaning they
cannot be assigned to a specific enzyme, leaving gaps in metabolic pathways. Novel …
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
Reaction classification has often been considered an important task for many different
applications, and has traditionally been accomplished using hand-coded rule-based …
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 …
pharmacodynamic properties of drug-like small-molecule scaffolds by modulating their …
A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks
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 …
malignant transformation. However, this view has changed through the recently described …