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Machine Learning Quantum Mechanical/Molecular Mechanical Potentials: Evaluating Transferability in Dihydrofolate Reductase-Catalyzed Reactions.
J Chem Theory Comput
January 2025
Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States.
Integrating machine learning potentials (MLPs) with quantum mechanical/molecular mechanical (QM/MM) free energy simulations has emerged as a powerful approach for studying enzymatic catalysis. However, its practical application has been hindered by the time-consuming process of generating the necessary training, validation, and test data for MLP models through QM/MM simulations. Furthermore, the entire process needs to be repeated for each specific enzyme system and reaction.
View Article and Find Full Text PDFAdjustment of Molecular Sorption Equilibrium on Catalyst Surface for Boosting Catalysis.
Acc Chem Res
January 2025
Key Lab of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.
ConspectusFor chemical reactions with complex pathways, it is extremely difficult to adjust the catalytic performance. The previous strategies on this issue mainly focused on modifying the fine structures of the catalysts, including optimization of the geometric/electronic structure of the metal nanoparticles (NPs), regulation of the chemical composition/morphology of the supports, and/or adjustment of the metal-support interactions to modulate the reaction kinetics on the catalyst surface. Although significant advances have been achieved, the catalytic performance is still unsatisfactory.
View Article and Find Full Text PDFContext-dependent similarity analysis of analogue series for structure-activity relationship transfer based on a concept from natural language processing.
J Cheminform
January 2025
Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany.
Analogue series (AS) are generated during compound optimization in medicinal chemistry and are the major source of structure-activity relationship (SAR) information. Pairs of active AS consisting of compounds with corresponding substituents and comparable potency progression represent SAR transfer events for the same target or across different targets. We report a new computational approach to systematically search for SAR transfer series that combines an AS alignment algorithm with context-depending similarity assessment based on vector embeddings adapted from natural language processing.
View Article and Find Full Text PDFResilience in maternal, newborn, and child health in low- and middle-income countries: findings from a scoping review.
Reprod Health
January 2025
Department of Global Health, University of Warwick, Coventry, UK.
Objectives: The research objectives were to identify and synthesise prevailing definitions and indices of resilience in maternal, newborn, and child health (MNCH) and propose a harmonised definition of resilience in MNCH research and health programmes in low- and middle-income countries (LMICs).
Design: Scoping review using Arksey and O'Malley's framework and a Delphi survey for consensus building.
Participants: Mothers, new-borns, and children living in low- and middle-income countries were selected as participants.
Derivation and validation of a clinical predictive model for longer duration diarrhea among pediatric patients in Kenya using machine learning algorithms.
BMC Med Inform Decis Mak
January 2025
Kenya Medical Research Institute- Center for Global Health Research (KEMRI-CGHR), P.O Box 1578-40100, Kisumu, Kenya.
Background: Despite the adverse health outcomes associated with longer duration diarrhea (LDD), there are currently no clinical decision tools for timely identification and better management of children with increased risk. This study utilizes machine learning (ML) to derive and validate a predictive model for LDD among children presenting with diarrhea to health facilities.
Methods: LDD was defined as a diarrhea episode lasting ≥ 7 days.
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