Glycoinformatics-assisted Structure Modeling Service
Your Trusted Partner in Glycobiology: Comprehensive Structure Modeling
Glycans, usually in the form of glycoconjugates, are involved in several pathological and physiological processes such as cell differentiation and recognition. Based on extensive experience in Analysis and Prediction, CD BioGlyco provides a comprehensive, efficient, and accurate glycoinformatics-assisted structural modeling service.
We offer customized solutions that are readily adapted to meet the specific research needs of research scholars. Through our analysis of the structure of the glycoconjugate, we help gain meaningful insights to advance their related research. Our glycoinformatics-assisted structural analysis service consists of two main parts:
Structure detection
We use different methods and techniques to detect the structure of glycoproteins, glycolipids, etc., including sequences, monosaccharides, branching points, glycosidic bonds, modifications, etc.
- Liquid chromatography-mass spectrometry (LC-MS)
- Capillary electrophoresis (CE)
- Nuclear magnetic resonance (NMR)
- Electrospray ionization mass spectrometry (ESI-MS)
- Gas chromatography (GC)
- X-ray crystallography
- Cryogenic electron microscopy
- Other analytical methods
Structure modeling
We have senior bioinformaticians with rich practical experience in database mining, structural bioinformatics, and other fields. Our team validates, processes, and analyzes experimental data, and other related data based on structural databases, web, tools, and software according to the research objectives of our clients. We aim to help better understand the role of glycans in various biological processes by modeling and processing structural data.
- Molecular dynamics (MD) and molecular mechanics(MM) calculations
- Semi-empirical methods
- Monte Carlo simulations
- Others
We also offer our clients the following options for structural analysis services:
Publication Data
Technology: Computational modeling
Journal: Frontiers in Immunology
IF: 4.716
Published: 2018
Results: Knowledge of the structures of the E1 and E2 envelope glycoproteins of the hepatitis C virus is useful for vaccine development. This paper summarizes studies in modeling the structure of E2 glycoproteins, assembly of E1E2 heterodimers, etc. In addition to this, comparisons of structural models of complete E1E2 heterodimers, modeling of glycosylation, etc., are also discussed in this paper. These computational modeling approaches provide methodological support for glycoprotein structure modeling.
Fig.1 Models of E1E2 heterodimeric assembly. (Li, et al., 2020)
Applications
- Structural modeling of glycoproteins, glycolipids, proteoglycans, etc., is used to study the correlation between structure and function.
- Glycans are associated with cancer, immune diseases, etc. Structural modeling of glycoproteins, proteoglycans, etc., helps to explore the mechanisms of these diseases and to study new therapeutic approaches.
- Glycans are involved in several processes in organisms. Structural modeling of glycoproteins, glycolipids, proteoglycans, etc., is used to probe cell signaling, immunity, and other physiological processes.
Advantages
- Our bioinformatics team has extensive experience in structural bioinformatics and database mining.
- We utilize state-of-the-art software tools and algorithms to process structural data.
- We specialize in integrating multiple data types to enable reliable modeling of structures such as glycoproteins, glycolipids, and proteoglycans.
Frequently Asked Questions
- How to process the structured data obtained by LC-MS?
- Data preprocessing: Raw LC-MS data are preprocessed and denoised to improve data quality and accuracy of analysis results.
- Feature extraction: Meaningful features from complex mass spectrometry data are extracted.
- Data alignment: This is a necessary step to ensure that data can be compared and analyzed between samples.
- Characterization: Characterization can be achieved through the use of statistical model-based methods, standard curve methods, or internal standard methods.
- Data interpretation and statistical analysis: Data are interpreted and statistically analyzed to obtain information related to differences between samples.
- What tools are being used for model construction and analysis?
- Web-based tools and stand-alone software packages have been developed to facilitate the handling of 3D structures of carbohydrates, among others.
- GLYCAM-Web: It provides tools for glycan structure prediction, glycoprotein 3D model generation, docking, and grafting.
- CHARMM-GUI Modeler: It provides options for 3D structure generation and modeling of glycans in glycoproteins and glycolipids, which can be used in combination with other tools.
- In addition to this, Glycosylated and Rosetta Carbohydrate can be also used for modeling glycoproteins, glycan-glycoprotein docking, etc.
CD BioGlyco, a leading technology company, offers a wide range of services for structural modeling of glycoproteins, glycolipids, GAGs, and more. Please feel free to contact us for more information, if you have questions or needs in structural modeling.
Reference
- Guest, J.D.; Pierce, B.G. Computational modeling of hepatitis C virus envelope glycoprotein structure and recognition. Frontiers in Immunology. 2018, 9: 1117.
For research use only. Not intended for any diagnostic use.
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