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 a pathogenic variant in NF1 is diagnostic for neurofibromatosis, but is often impossible at the moment of variant detection due to many factors including allelic heterogeneity, sequence homology, and the lack of functional assays. C...
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...
Missense mutations can disrupt the structure and function of membrane proteins, potentially impairing key biological processes and leading to various human diseases. However, existing computational methods primarily focus on binary pathogenicity clas...
Proceedings of the National Academy of Sciences of the United States of America
May 2, 2025
Understanding the effects of missense mutations or single amino acid variants (SAVs) on protein function is crucial for elucidating the molecular basis of diseases/disorders and designing rational therapies. We introduce here , a machine learning too...
The right classification of variants is the key to pre-symptomatic detection of disease and conducting preventive actions. Since BRCA1 has a high incidence and penetrance in breast and ovarian cancers, a high-performance predictive tool can be employ...
Journal of chemical information and modeling
Apr 14, 2025
Missense mutations in oncogenic proteins that are concurrently associated with neurodevelopmental disorders have garnered significant attention. Phosphatase and tensin homologue (PTEN) serves as a paradigmatic model for mapping its mutational landsca...
There is a great discrepancy between the clinical categorization of MEFV gene variants and in silico tool predictions. In this study, we developed a seven-tier classification system for MEFV missense variants of unknown significance and recommended a...
We use a combination of Brownian dynamics (BD) simulation results and deep learning (DL) strategies for the rapid identification of large structural changes caused by missense mutations in intrinsically disordered proteins (IDPs). We used ∼6500 IDP s...
The Signal Transducer and Activator of Transcription 1 () gene is an essential component of the JAK-STAT signaling pathway. This pathway plays a pivotal role in the regulation of different cellular processes, including immune responses, cell growth,...
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