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Summary: Comparisons of protein structures are critical for developing novel protein designs, annotating protein functions and predicting protein structure. The template modeling score (TM-score) is a widely used but computationally expensive measure of protein similarity that is applicable to a wide variety of structural biology problems. We introduce TMQuery-a continuously updated database containing over eight billion pre-computed TM-score values for every pair of proteins in the Protein Data Bank, allowing researchers to quickly query and download TM-scores via a web interface.
Availability And Implementation: Publicly available at https://tmquery.gsk.com/.
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http://dx.doi.org/10.1093/bioinformatics/btac044 | DOI Listing |
Adv Mater
September 2025
Department of Biomedical Engineering, University of Strathclyde, Glasgow, G4 0NW, UK.
Vasculature plays a crucial role in tissue engineering since it is essential for maintaining tissue viability by efficient nutrient and oxygen exchange as well as waste removal. The creation of biomimetic vascular networks is therefore critical for the development of functional tissue constructs. Sacrificial biofabrication has emerged as an effective method for engineering vascular structures by creating temporary templates that are subsequently removed to form well-defined vascular channels.
View Article and Find Full Text PDFIEEE Trans Comput Biol Bioinform
September 2025
Deciphering the three-dimensional structure of proteins remains a grand challenge in biology and medicine, as it holds the key to understanding their biological functions and facilitating drug discovery. In this paper, we introduce DECIPHER (Deep Encoding of Cellular Interactions and Protein HiErarchical Representation), a novel deep graph learning framework for protein structure prediction. By representing proteins as graphs, where residues and atoms serve as nodes and their interactions form edges, we capture the intricate spatial relationships within these complex biomolecules.
View Article and Find Full Text PDFCochrane Database Syst Rev
September 2025
Department of Family Medicine, University of Alberta, Edmonton, Alberta, Canada.
Background: Opioid use disorder (OUD) is commonly treated in specialized care settings with long-acting opioid agonists, also known as opioid agonist therapy, or OAT. Despite the rise in opioid use globally and evidence for a 50% reduction in mortality when OAT is employed, the proportion of people with OUD receiving OAT remains small. One initiative to improve the access and uptake of OAT could be to offer OAT in a primary care setting; primary care clinics are more numerous, might reduce the visibility and potential stigma of receiving treatment for OUD, and may facilitate the care of other medical conditions that are unrelated to OUD.
View Article and Find Full Text PDFColloids Surf B Biointerfaces
August 2025
School of Stomatology, Qingdao University, Qingdao 266023, PR China; Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao 266003, PR China.
White spot lesions (WSLs) are the most common complication of orthodontic treatment, compromising dental health and significantly affecting aesthetics. To address this clinical challenge, this study aims to develop a dual-functional therapeutic strategy that simultaneously promotes the remineralization of demineralized enamel and inhibits the activity of cariogenic bacteria, thereby achieving effective prevention and treatment of WSLs. A hollow double-shell structured CuO@N/C nanozyme (H-CuO@N/C) was synthesized using a one-step hydrothermal method.
View Article and Find Full Text PDFIntroduction: Precise prediction of pathological complete response (pCR) following neoadjuvant chemoradiotherapy (nCRT) in rectal cancer may identify candidates for non-operative management. The optimal selection of diagnostic tools is therefore of major clinical importance.
Methods: Clinical, laboratory, endoscopic and radiological data of patients with rectal cancer treated with nCRT and surgery at an academic medical center from 2010 to 2020 were retrospectively collected.