Due to the rising number of solved protein structures, computer-based techniques for automatic protein functional annotation and classification into families are of high scientific interest. DoGSiteScorer automatically calculates global descriptors for self-predicted pockets based on the 3D structure of a protein. Protein function predictors on three levels with increasing granularity are built by use of a support vector machine (SVM), based on descriptors of 26632 pockets from enzymes with known structure and enzyme classification. The SVM models represent a generalization of the available descriptor space for each enzyme class, subclass, and substrate-specific sub-subclass. Cross-validation studies show accuracies of 68.2% for predicting the correct main class and accuracies between 62.8% and 80.9% for the six subclasses. Substrate-specific recall rates for a kinase subset are 53.8%. Furthermore, application studies show the ability of the method for predicting the function of unknown proteins and gaining valuable information for the function prediction field.
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http://dx.doi.org/10.1002/prot.24205 | DOI Listing |
Acta Biomater
January 2025
Department of Industrial Engineering, School of Engineering and Architecture, University of Bologna, Viale del Risorgimento 2, 40136, Bologna, Italy. Electronic address:
Intervertebral disc (IVD) degeneration is suspected to affect the distribution of stress and strain near the vertebral endplates and in the underlying bone. This scenario is worsened by the presence of metastatic lesions on the vertebrae (primarily thoracic vertebrae (60-80%)) which increase the risk of fracture. As such, this study aimed to evaluate the effect of IVD degeneration on the internal volumetric strains and failure modes of human metastatic vertebral bodies.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA.
A couple presented to the office with an apparently healthy infant for a thorough clinical assessment, as they had previously lost two male children to a neurodegenerative disorder. They also reported the death of a male cousin abroad with a comparable condition. We aimed to evaluate a novel coding pathogenic variant c.
View Article and Find Full Text PDFInt J Biol Macromol
January 2025
College of Forestry, Henan Agricultural University, Zhengzhou 450046, China. Electronic address:
In this study, we fully sequenced and analyzed the genome of strain 12219 and identified it as Streptomyces thermocarboxydus. The genome contained a single linear chromosome, 6,950,031 bp in size, with a GC content of 72.21 %.
View Article and Find Full Text PDFInt J Biol Macromol
January 2025
School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, PR China; Hubei Shizhen Laboratory, Wuhan 430061, PR China; Key Laboratory of·Traditional, Chinese Medicine Resources and Traditional Chinese Medicine Formulas, Hubei University of Chinese Medicine, Wuhan 430065, PR China. Electronic address:
Klebsiella pneumoniae exhibits extensive glycohydrolase activity in the gut microbiota. However, there are few studies on glucomannanase of Klebsiella pneumoniae. This study cloned and characterized a bifunctional mannanase/glucanase (GH8-3995) of K.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 10120, Thailand.
A single-component flavin-dependent halogenase, AetF, has emerged as an attractive biocatalyst for catalyzing halogenation. However, its flavin chemistry remains unexplored and cannot be predicted due to its uniqueness in sequence and structure compared to other flavin-dependent monooxygenases. Here, we investigated the flavin reactions of AetF using transient kinetics.
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