Jonathan D. Hirst
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View article: Explainable random forest predictions of polyester biodegradability using high-throughput biodegradation data
Explainable random forest predictions of polyester biodegradability using high-throughput biodegradation data Open
A new high-throughput enzymatic biodegradation assay has been developed, and the data have been used to train a machine learning model to predict polyester biodegradability and explain how structural features influence biodegradability.
View article: Challenges and Advances in the Simulation of Targeted Covalent Inhibitors Using Quantum Computing
Challenges and Advances in the Simulation of Targeted Covalent Inhibitors Using Quantum Computing Open
Targeted covalent inhibitors represent a promising class of drugs that form specific chemical bonds with their biological targets. There are a multitude of molecular systems where covalent inhibitors could address human health challenges. …
View article: Enhancing Monte Carlo Tree Search for Retrosynthesis
Enhancing Monte Carlo Tree Search for Retrosynthesis Open
Computer-Assisted Synthesis Programs are increasingly employed by organic chemists. Often, these tools combine neural networks for policy prediction with heuristic search algorithms. We propose two novel enhancements, which we call eUCT an…
View article: AI4Green4Students: Promoting Sustainable Chemistry in Undergraduate Laboratories with an Electronic Lab Notebook
AI4Green4Students: Promoting Sustainable Chemistry in Undergraduate Laboratories with an Electronic Lab Notebook Open
AI4Green is an open-source, machine-learning-powered electronic laboratory notebook (ELN) developed to help chemists mitigate environmental impacts, particularly within the pharmaceutical sector. This study presents AI4Green4Students, a pe…
View article: Practical Guidelines for Optimising Free Energy Calculations Using Thermodynamic Integration
Practical Guidelines for Optimising Free Energy Calculations Using Thermodynamic Integration Open
Free energy calculations have become valuable in structure-based drug design, but their accuracy and reliability remain significant challenges. Here, we present an automated workflow for free energy estimation built with AMBER20, alchemlyb…
View article: Challenges and Advances in the Simulation of Targeted Covalent Inhibitors Using Quantum Computing
Challenges and Advances in the Simulation of Targeted Covalent Inhibitors Using Quantum Computing Open
Targeted covalent inhibitors represent a promising class of drugs that form specific chemical bonds with their biological targets. There are a multitude of molecular systems where covalent inhibitors could address human health challenges. …
View article: Rega: A Platform for the Prediction of the Regioselectivity of C–H Functionalisation Reactions
Rega: A Platform for the Prediction of the Regioselectivity of C–H Functionalisation Reactions Open
Sulfinate-mediated radical C–H functionalisation reactions are widely used for the modification and diversification of scaffolds in drug discovery. However, prediction of the regiochemistry can be challenging. There may be multiple sites o…
View article: Interactive Knowledge-Based Kernel PCA for Solvent Selection
Interactive Knowledge-Based Kernel PCA for Solvent Selection Open
Selecting more sustainable solvents is a crucial component to mitigating the environmental impacts of chemical processes. Numerous tools have been developed to address this problem within the pharmaceutical industry, employing data-driven …
View article: Enhancing Monte Carlo Tree Search for Retrosynthesis
Enhancing Monte Carlo Tree Search for Retrosynthesis Open
Computer-Assisted Synthesis Programs are increasingly employed by organic chemists. Often, these tools combine neural networks for policy prediction with heuristic search algorithms. We propose two novel enhancements, which we call eUCT an…
View article: DyeDactic: towards biosynthetic alternatives to artificial textile dyes
DyeDactic: towards biosynthetic alternatives to artificial textile dyes Open
Production and application of textile dyes using microorganisms represents an important step towards sustainable manufacturing. Although living organisms can produce numerous coloured substances, they frequently demonstrate poor dyeing per…
View article: AI4Green4Students: Promoting sustainable chemistry in undergraduate laboratories with an electronic lab notebook
AI4Green4Students: Promoting sustainable chemistry in undergraduate laboratories with an electronic lab notebook Open
AI4Green is an open-source, machine-learning-powered electronic laboratory notebook (ELN) developed by our research group to help chemists mitigate environmental impacts, particularly within the pharmaceutical sector. This study presents A…
View article: Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors Open
Myotonic dystrophy type I (DM1) is the most common form of adult muscular dystrophy and is a severe condition with no treatment currently available. Recently, small-molecule ligands have been developed as targeted covalent inhibitors that …
View article: Theoretical Study on the Biosynthesis of the Mandapamates: Mechanistic Insights Using Density Functional Theory
Theoretical Study on the Biosynthesis of the Mandapamates: Mechanistic Insights Using Density Functional Theory Open
Density functional theory (B3LYP-D3(BJ) and ωB97XD) calculations have been used to assess the stereochemical outcomes of the proposed transannular [4 + 2] cycloaddition pathway for the biosynthesis of mandapamate and isomandapamate from ma…
View article: An Improved Diabatization Scheme for Computing the Electronic Circular Dichroism of Proteins
An Improved Diabatization Scheme for Computing the Electronic Circular Dichroism of Proteins Open
We advance the quality of first-principles calculations of protein electronic circular dichroism (CD) through an amelioration of a key deficiency of a previous procedure that involved diabatization of electronic states on the amide chromop…
View article: Artificial intelligence for small molecule anticancer drug discovery
Artificial intelligence for small molecule anticancer drug discovery Open
The advent of big data has allowed AI to penetrate and enable innovations in almost every stage of medicine discovery, transforming the landscape of oncology research through the development of state-of-the-art algorithms and models. Despi…
View article: Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors Open
Myotonic dystrophy type I (DM1) is the most common form of adult muscular dystrophy and is a severe condition with no treatment currently available. Recently, small-molecule ligands have been developed that have some selectivity for and co…
View article: Applications of Quantum Chemistry in Biomimetic Syntheses of Polycyclic Furanocembrane Derivatives
Applications of Quantum Chemistry in Biomimetic Syntheses of Polycyclic Furanocembrane Derivatives Open
This account summarizes the guidance provided by quantum chemical calculations towards the biomimetic syntheses of polycyclic marine furanocembrane derivatives. Polycyclic furanocembrane derivatives are a group of structurally complex and …
View article: Discovery of novel SOS1 inhibitors using machine learning
Discovery of novel SOS1 inhibitors using machine learning Open
Machine learning enabled ligand-based virtual screening is a valuable tool in discovering effective SOS1 inhibitors.
View article: Optimizing Excipient Properties to Prevent Aggregation in Biopharmaceutical Formulations
Optimizing Excipient Properties to Prevent Aggregation in Biopharmaceutical Formulations Open
Excipients are included within protein biotherapeutic solution formulations to improve colloidal and conformational stability but are generally not designed for the specific purpose of preventing aggregation and improving cryoprotection in…
View article: Theoretical Analysis of Divalent Cation Effects on Aptamer Recognition of Neurotransmitter Targets
Theoretical Analysis of Divalent Cation Effects on Aptamer Recognition of Neurotransmitter Targets Open
Aptamer-based sensing of small molecules such as dopamine and serotonin in the brain, requires characterization of the specific aptamer sequences in solutions mimicking the in vivo environment with physiological ionic concentrations. In pa…
View article: Synergistic engineering of heteronuclear Ni-Ag dual-atom catalysts for high-efficiency CO2 electroreduction with nearly 100% CO selectivity
Synergistic engineering of heteronuclear Ni-Ag dual-atom catalysts for high-efficiency CO2 electroreduction with nearly 100% CO selectivity Open
Single-atom catalysts (SACs) have emerged as attractive materials for the electrocatalytic carbon dioxide reduction (ECO2R). Dual-atom catalysts (DACs), an extension of SACs, exhibit more compelling functionalities due to the synergistic e…
View article: Optimising excipient properties to prevent aggregation in biopharmaceutical formulations
Optimising excipient properties to prevent aggregation in biopharmaceutical formulations Open
Excipients are included within protein biotherapeutic solution formulations to improve colloidal and conformational stability, but are generally not designed for the specific purpose of preventing aggregation and improving cryoprotection i…