Proceedings of the National Academy of Sciences of the United States of America
Aug 19, 2025
Foundation models in biology-particularly protein language models (PLMs)-have enabled ground-breaking predictions in protein structure, function, and beyond. However, the "black-box" nature of these representations limits transparency and explainabil...
Journal of chemical information and modeling
Aug 18, 2025
With the remarkable stride in computing power and advances in Molecular Dynamics (MD) simulation programs, the crucial challenge of storing and sharing large biomolecular simulation data sets has emerged. By leveraging AutoEncoders, a type of artific...
Journal of chemical information and modeling
Aug 12, 2025
Accurate modeling of protein-peptide interactions is essential for understanding fundamental biological processes and designing peptide-based drugs. However, predicting the complex structures of these interactions remains challenging, primarily due t...
BACKGROUND: Drug development is a time-consuming and costly endeavor, and utilizing computer-aided methods to predict drug-target affinity (DTA) can significantly accelerate this process. The key to accurate DTA prediction lies in selecting appropria...
Inferring protein function is a fundamental and long-standing problem in biology. Laboratory experiments in this field are often expensive, and therefore large-scale computational protein inference from readily available amino acid sequences is neede...
Accurate prediction of the functional impact of missense variants is important for disease gene discovery, clinical genetic diagnostics, therapeutic strategies, and protein engineering. Previous efforts have focused on predicting a binary pathogenici...
Journal of chemical information and modeling
Jul 25, 2025
Machine learning has become an essential tool in computational drug design, enabling models to uncover patterns in molecular data and predict protein-ligand interactions. This study introduces a novel approach by integrating persistence images with M...
Journal of chemical information and modeling
Jul 25, 2025
To understand the benefits and drawbacks of 3D combinatorial and deep learning generators, a novel benchmark was created focusing on the recreation of important protein-ligand interactions and 3D ligand conformations. Using the BindingMOAD data set w...
Accurate protein expression in human immune cells is essential for appropriate cellular function. The mechanisms that define protein abundance are complex and are executed on transcriptional, posttranscriptional, and posttranslational levels. Here, w...
Journal of physics. Condensed matter : an Institute of Physics journal
Jul 23, 2025
This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and analysis f...
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