Physical chemistry chemical physics : PCCP
Jan 14, 2026
Recent advances in machine learning and self-supervised deep language modeling have made it possible to accurately predict protein structural properties. Most existing models and pretraining methods leverage evolutionary information in multiple seque...
Journal of the American Society for Mass Spectrometry
Dec 21, 2025
Recent advances in ion mobility spectrometry have enabled the measurement of rotationally averaged collisional cross-sectional area (CCS) for millions of peptides as part of routine proteomic mass spectrometry workflows. One of the most striking find...
Journal of agricultural and food chemistry
Dec 10, 2025
The diversity and functions of metallothioneins (MTs) in Archaea remain poorly understood. This study identifies 180 archaeal MTs from 406 genomes, revealing distinct evolutionary lineages and structural diversity. Phylogenetic analysis suggests a no...
Journal of chemical information and modeling
Dec 3, 2025
Developing effective computational representations of protein sequences is crucial for advancing diverse areas of computational biology and bioinformatics. Ideal representations must be computationally efficient, scalable, informative, flexible acros...
Identification of virulence factors (VFs) is critical for expanding our knowledge on bacterial pathogenesis and also for developing targeted strategies for the prevention and treatment of related infectious diseases. Understanding virulence factors r...
Journal of chemical information and modeling
Nov 17, 2025
Predicting protein function from its primary sequence is a fundamental challenge in computational biology. While deep learning has excelled, the optimal representation of sequence data remains an open question. This study explores protein sonificatio...
Adverse drug events represent a key challenge in public health, especially concerning drug safety profiling and drug surveillance. Drug-drug interactions represent one of the most popular types of adverse drug events. Most computational approaches to...
Deep learning models show promise in accelerating the design and optimization of antimicrobial peptides (AMPs), but current methods face challenges, such as low success rates, or large virtual library scales. In this study, we introduce DLFea4AMPGen,...
Proceedings of the National Academy of Sciences of the United States of America
Oct 10, 2025
Adaptive differences in the thermal stabilities of enzyme structure and function play critical roles in establishing the thermal optima and limits of all organisms. Thus, understanding the mechanisms underlying these adaptations can yield insights in...
The catalytic activity of enzymes is intricately determined by their amino acid sequences and assay conditions, particularly temperature. Navigating the complex interplay among sequence, temperature, and catalytic function is crucial for unlocking a ...
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