Glycoinformatics-assisted Glycan-Molecular Interaction Analysis Service
Glycoinformatics-assisted Analysis: The Future of Glycan-Molecular Interaction Studies
CD BioGlyco is committed to providing glycoinformatics-assisted glycan-molecular interaction analysis service, a comprehensive service that combines glycobiology and bioinformatics. Below is a detailed category description of the service.
We use molecular dynamics simulation technology to simulate the dynamic behavior of sugar chain molecules at the atomic scale. Molecular dynamics simulation simulates the motion trajectory of sugar chain molecules under specific conditions by solving Newton's equations of motion and then analyzes their conformational changes, stability, and interactions with other molecules in the biological environment.
Quantum mechanics/molecular mechanics (QM/MM) simulation service combines the advantages of quantum mechanics (QM) and molecular mechanics (MM) to provide a more accurate description of sugar chain molecules and their interactions with the surrounding environment. The QM method can handle changes in electronic structure, while the MM method is suitable for handling the overall conformation and energy changes of macromolecular systems. The combination of the two enables us to more accurately simulate the behavior of sugar chains in complex biological systems.
Our glycoinformatics-assisted glycan-molecular interaction analysis services are designed to provide a deep understanding of interactions between glycans and other molecules. Our services include but are not limited to the following aspects.
Glycan structure analysis
Glycan sequence analysis: We use mass spectrometry (MS), nuclear magnetic resonance (NMR), and other technologies to accurately analyze the composition and sequence of glycans, providing basic data for subsequent interaction analysis.
Three-dimensional structure prediction of glycans: Based on the sequence information of glycans, we use computational simulation methods to predict their three-dimensional structures, providing a model for simulating interactions between glycans and other molecules.
Prediction of glycan-molecule interactions
Molecular docking simulation: We use bioinformatics software to simulate the docking process of glycans and potential interacting molecules (such as proteins and antibodies) to predict possible binding sites and interaction modes.
Interaction energy calculation: We calculate the interaction energy between glycans and molecules to evaluate the stability and affinity of the interaction, providing a theoretical basis for experimental verification.
Verification of glycan-molecule interactions
Affinity experiment: We use surface plasmon resonance (SPR), fluorescence polarization, and other technologies to experimentally verify the affinity between glycans and molecules.
Functional verification: We verify the impact of interactions between glycans and molecules on biological functions in cells or animal models.
Data analysis and reporting
Data analysis: We perform statistical analysis on experimental data, extract key information, and provide scientific explanations for experimental results.
Report writing: We write detailed experimental reports based on client needs and provide clients with comprehensive service support.
Publication Data
Technology: LectinOracle model development
Journal: Advanced Science
IF: 15.1
Published: 2022
Results: The authors presented LectinOracle, a model that blended transformer-based representations for proteins and graph convolutional neural networks for glycans for interaction prediction. They utilized a curated data set comprising 564,647 unique protein-glycan interactions, showing that LectinOracle predictions agreed well with literature-annotated specificities across various lectins. They demonstrated using a range of specialized glycan arrays that the LectinOracle predictions were robust and could generalize to new glycans and lectins. The findings matched both qualitatively and quantitatively with experimental data.
Fig.1 LectinOracle predicts binding of lectins to various types of glycan arrays. (Lundstrøm,et al., 2022)
Applications
- Glycoinformatics-assisted glycan-molecular interaction analysis can be used to systematically study the relationship between the structure and function of glycans and reveal the biological significance of glycans in organisms.
- Glycoinformatics-assisted glycan-molecular interaction analysis can be used to evaluate the affinity of drug candidates to glycan chain targets, thereby screening out compounds with potential medicinal effects.
- Glycoinformatics-assisted glycan-molecular interaction analysis can be used to design vaccines that induce stronger and longer-lasting immune responses.
- Glycoinformatics-assisted glycan-molecular interaction analysis can be used to manipulate glycosylation patterns to optimize in vitro growth of certain cell types.
Advantages of Us
- We use advanced glycoinformatics technology combined with efficient data tools to quickly and accurately analyze the interactions between glycans and other molecules.
- We provide highly customized glycoinformatics-assisted glycan-molecular interaction analysis services. Whether it is sample processing, data analysis methods, or reporting formats, we customize them according to our client’s specific needs.
- Our scientific research team is composed of experts in the fields of glycobiology and bioinformatics. They have rich experience and deep professional knowledge to ensure the accuracy and reliability of analytical results.
- We provide clients with comprehensive technical support, including explanations of data analysis methods, interpretation of results, and subsequent research suggestions.
Frequently Asked Questions
- How does your glycoinformatics-assisted glycan-molecular interaction analysis service work?
- Our glycoinformatics-assisted glycan-molecular interaction analysis service uses advanced bioinformatics and computational simulation technology. We first obtain the structural information of glycan through glycomic experimental methods and then use bioinformatics software to analyze the relationship between glycans and other molecules (such as proteins, nucleic acids, lipids, etc.). Through computational simulation, we reveal the interaction mechanism between glycans and molecules, providing an important basis for drug development and disease mechanism research.
- Can I make special requests or customized needs during the service?
- Of course! We attach great importance to client needs and feedback and provide customized service solutions based on specific requirements. Whether it is experimental design, data analysis, or result interpretation, we fully communicate and negotiate with clients to ensure that the service plan meets expectations and needs.
- How do I stay in touch and communicate with your service team?
- We attach great importance to communication and contact with our clients. During the project, we designate a professional team to connect with clients and answer your questions and feedback in a timely manner. At the same time, we provide a variety of contact methods such as telephone, email, and online meetings so that clients keep in touch and communicate with us at any time. We do our best to provide you with excellent service and support.
Through glycoinformatics-assisted glycan-molecular interaction analysis service at CD BioGlyco, clients can fully understand the interactions between glycans and other molecules, providing strong support for research in drug development, disease research, and other fields. We look forward to working with you to advance the field of glycobiology. Please feel free to contact us if you are interested in our glycoinformatics-assisted glycan-molecular interaction analysis service.
Reference
- Lundstrøm, J.; et al. LectinOracle: a generalizable deep learning model for lectin–glycan binding prediction. Advanced Science. 2022, 9(1): 2103807.
For research use only. Not intended for any diagnostic use.
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