Ubiquitination Prediction Service
Understanding post-translational modifications (PTMs) is crucial. One of the most important and complex PTMs is ubiquitination–a process that plays a pivotal role in regulating protein stability, cellular signaling, and metabolic processes. At CD ComputaBio, we specialize in ubiquitination prediction, offering comprehensive computational modeling services that help researchers uncover critical insights into cellular functions and disease mechanisms. Our state-of-the-art technology and expert team are dedicated to providing accurate predictions that pave the way for groundbreaking research and therapeutic advancements.
Introduction to Ubiquitination
Ubiquitination is the attachment of ubiquitin molecules to a target protein, a process that can signal protein degradation or alter its activity and localization. This dynamic modification is fundamental to various biological processes, including cell cycle regulation, DNA repair, and immune response. Dysregulation of ubiquitination has been implicated in numerous diseases, including cancer, neurodegenerative disorders, and autoimmune diseases. With the increasing volume of biological data, researchers face the challenge of efficiently predicting ubiquitination sites and understanding their functional implications.
Figure 1. Ubiquitination Prediction. (Liu Y, et al. 2021)
Our Service
At CD ComputaBio, we offer a range of specialized services designed to meet the diverse needs of researchers and institutions. Our core feature services include:
Ubiquitination Site Prediction
We provide cutting-edge algorithms for accurately predicting ubiquitination sites on protein sequences. Our models integrate machine learning techniques, sequence-derived features, and molecular interaction data to enhance prediction accuracy.
Functional Annotation of Ubiquitinated Proteins
Understanding the biological implications of ubiquitination is essential for translating predictions into meaningful insights. Our functional annotation service links predicted ubiquitination sites to biological pathways, cellular processes, and disease associations, providing a comprehensive overview of their potential roles.
Structural-Based Ubiquitination Prediction
Our structural-based ubiquitination prediction service utilizes the three-dimensional structures of proteins. We analyze the surface properties, conformational flexibility, and the presence of binding pockets on proteins that may be involved in ubiquitination-related interactions.
Disease-Associated Ubiquitination Prediction
CD ComputaBio focuses on predicting ubiquitination events that are relevant to specific diseases. We analyze genomic and proteomic data from disease-affected tissues or cells and identify proteins that may have abnormal ubiquitination patterns in disease states.
Software We Use
PyMOL
This software assists in assessing the spatial interactions between ubiquitin and target proteins, helping to elucidate the mechanisms of ubiquitination in biological systems.
Rosetta
Rosetta is a powerful software suite for protein structure prediction and analysis. We use Rosetta for structure-based ubiquitination prediction
Approaches to Ubiquitination Prediction
Structural Bioinformatics
Understanding protein structure is vital in predicting ubiquitination interactions. Our structural bioinformatics approach utilizes 3D protein structures to assess how ubiquitin interacts with target proteins.
Sequence-Based Approaches
We rely on sequence-based approaches that analyze the primary amino acid sequence of proteins. These approaches use machine learning algorithms, such as neural networks and support vector machines.
hybrid Approaches
These approaches take advantage of the strengths of both methods, using sequence information to narrow down the search space and then using structure information to refine the prediction.
Advantages of Our Services
Ubiquitination prediction is a complex but essential task in understanding the regulatory mechanisms of proteins and their implications in various biological processes and diseases. CD ComputaBio offers a comprehensive range of services in this area, leveraging different approaches, advanced software tools, and a team of experts. Our focus on customized solutions, high-quality predictions, and timely delivery makes us an ideal partner for researchers and organizations involved in ubiquitination-related studies. Contact us to learn more about our services.
References:
- Liu Y, Jin S, Song L, et al. Prediction of protein ubiquitination sites via multi-view features based on eXtreme gradient boosting classifier. Journal of Molecular Graphics and Modelling, 2021, 107: 107962.
- Pourmirzaei M, Ramazi S, Esmaili F, et al. Machine learning-based approaches for ubiquitination site prediction in human proteins. BMC bioinformatics, 2023, 24(1): 449.
* For Research Use Only.
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