Identifying alternative indications for known drugs is important for the pharmaceutical industry. Many computational methods have been proposed for predicting unknown associations between drugs and target proteins associated with diseases. To produce better prediction, researchers should not only develop accurate algorithms but identify good features that reflect intracellular systems. In this paper, we proposed a novel method for exploiting protein localization. We generated localization vectors (LVs) from protein localization and propagated LVs through a protein interaction network to increase the coverage of the localization information. The LVs showed distinct patterns among targets of known drugs as well as independent characteristics compared to existing features. Based on the experimental results, we determined that including LVs improves cross-validation accuracy and, produces better novel predictions with real and independent clinical trial data. Moreover, the propagation of LVs showed a positive result that it can help in increasing the coverage of the prediction results.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1039/c5mb00306g | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Metabolically stable apelin analogs: development and functional role in water balance and cardiovascular function.
Clin Sci (Lond)
January 2025
Center for Interdisciplinary Research in Biology, College de France, Institut National de la Santé et de la Recherche Médicale, Paris, France.
Apelin, a (neuro) vasoactive peptide, plays a prominent role in controlling water balance and cardiovascular functions. Apelin and its receptor co-localize with vasopressin in magnocellular vasopressinergic neurons. Apelin receptors (Apelin-Rs) are also expressed in the collecting ducts of the kidney, where vasopressin type 2 receptors are also present.
View Article and Find Full Text PDFEnhanced O-glycosylation Site Prediction Using Explainable Machine Learning Technique with Spatial Local Environment.
Bioinformatics
January 2025
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
Motivation: The accurate prediction of O-GlcNAcylation sites is crucial for understanding disease mechanisms and developing effective treatments. Previous machine learning models primarily relied on primary or secondary protein structural and related properties, which have limitations in capturing the spatial interactions of neighboring amino acids. This study introduces local environmental features as a novel approach that incorporates three-dimensional spatial information, significantly improving model performance by considering the spatial context around the target site.
View Article and Find Full Text PDFDistinct TYRO3 and PROS1 expression levels contribute to preeclampsia pathogenesis.
Histochem Cell Biol
January 2025
Departments of Obstetrics and Gynecology, School of Medicine, Akdeniz University, Antalya, Turkey.
Preeclampsia (PE) is a severe placental complication occurring after the 20th week of pregnancy. PE is associated with inflammation and an increased immune reaction against the fetus. TYRO3 and PROS1 suppress inflammation by clearing apoptotic cells.
View Article and Find Full Text PDFEffects of Tasimelteon Treatment on Traumatic Brain Injury Through NRF-2/HO-1 and RIPK1/RIPK3/MLKL Pathways in Rats.
Mol Neurobiol
January 2025
Department of Pathology, Faculty of Veterinary Medicine, Burdur Mehmet Akif Ersoy University, Burdur, Turkey.
Secondary brain damageafter traumatic brain injury (TBI) involves oxidative stress, neuroinflammation, apoptosis, and necroptosis and can be reversed by understanding these molecular pathways. The objective of this study was to examine the impact of tasimelteon (Tasi) administration on brain injury through the nuclear factor erythroid 2-related factor 2 (NRF-2)/heme oxygenase-1 (HO-1) and receptor-interacting protein kinase 1 (RIPK1)/receptor-interacting protein kinase 3 (RIPK3)/mixed lineage kinase domain-like (MLKL) pathways in rats with TBI. Thirty-two male Wistar albino rats weighing 300-350 g were randomly divided into four groups: the control group, trauma group, Tasi-1 group (trauma + 1 mg/kg Tasi intraperitoneally), and Tasi-10 group (trauma + 10 mg/kg Tasi intraperitoneally).
View Article and Find Full Text PDFHepatocyte Rho-associated kinase signaling is required for mice to survive experimental porphyria-associated liver injury.
Hepatol Commun
February 2025
Department of Surgery, University of California, San Francisco, San Francisco, California, USA.
Background: Rho-associated kinases 1 and 2 (ROCK1 and ROCK2) regulate critical cell functions, including actomyosin contractility, apoptosis, and proliferation. Some studies suggest that ROCK inhibition may serve as a treatment for liver fibrosis. More investigation is needed to understand the role of hepatocyte ROCK signaling in vivo, especially in the context of profibrotic liver injury.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!