GCduo: An Open-Source Software for GC × GC–MS Data Analysis

Chemistry, Analytical Chemistry, Computational Chemistry,
GC × GC–MS   multi-dimensional chromatography   metabolomics   chemometrics   PARAFAC   PARAFAC2   open-source software  

Academic Background and Research Motivation With the growing demand for the analysis of complex samples, chromatographic technologies—especially comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC×GC–MS)—have emerged as a powerhouse for untargeted metabolomics and related fields, demonstrating exceptional resolving p...

DockEM: An Enhanced Method for Atomic-Scale Protein–Ligand Docking Refinement Leveraging Low-to-Medium Resolution Cryo-EM Density Maps

Chemistry, Medicinal Chemistry, Computational Chemistry, Life Sciences, Biochemistry, Biophysics,
protein-ligand docking   cryo-EM   molecular docking   drug screening   structural biology  

Academic Background and Research Motivation In recent years, protein–ligand docking has rapidly developed as a core technology for virtual drug screening and structure-based drug discovery. Despite improvements in drug discovery efficiency through large-scale high-throughput screening technologies, new drug development still faces high costs, long ...

A Sparse Bayesian Committee Machine Potential for Oxygen-Containing Organic Compounds

Chemistry, Organic Chemistry, Physical Chemistry, Computational Chemistry, Chemical Engineering, Materials Science,
machine learning   Bayesian committee machine   oxygen-containing organic compounds   interatomic potentials   computational chemistry  

Academic Background In the fields of materials science and chemistry, understanding the properties of materials at the atomic level is crucial. However, traditional methods for calculating interatomic potentials, such as Density Functional Theory (DFT), while highly accurate, are computationally expensive and difficult to apply to large-scale syste...

GutBugDB: A Web Resource to Predict the Human Gut Microbiome-Mediated Biotransformation of Biotic and Xenobiotic Molecules

Chemistry, Medicinal Chemistry, Computational Chemistry, Information Science, Artificial Intelligence, Medicine, Gastroenterology, Pharmacy, Life Sciences, Biochemistry, Microbiology,
biotransformation   database   human gut microbiome   machine learning   xenobiotic metabolism  

In recent years, the significant role of the human gut microbiota (HGM) in the metabolism of drugs and nutrients has gradually been recognized. The gut microbiota not only affects the bioavailability of orally administered drugs but also participates in the biotransformation of drugs and bioactive molecules through its metabolic enzymes, thereby in...

Mechanistic Insights into Inactivating Mutations in the Proton-Coupled Folate Transporter (SLC46A1), and Compensatory Mutations that Restore Function

Chemistry, Physical Chemistry, Medicinal Chemistry, Computational Chemistry, Medicine, Life Sciences, Biochemistry, Genetics,
Proton-Coupled Folate Transporter   Inactivating Mutations   Functional Restoration   Molecular Dynamics Simulation   Hereditary Folate Malabsorption  

Research Background and Problem Statement Hereditary Folate Malabsorption (HFM) is a rare autosomal recessive disorder characterized by impaired intestinal absorption of folates and hindered transport across the choroid plexus into cerebrospinal fluid. This disease is caused by inactivating mutations in the gene encoding the Proton-Coupled Folate T...