Glycoscience Docking and Interaction Analysis Service
Unlocking the Secrets of Glycan-Protein Interactions for Breakthrough Discoveries
At CD BioGlyco, our glycoscience docking and interaction analysis service provides an advanced solution to study the interactions of glycans with proteins. It builds computational models and techniques to model and analyze glycans binding complex with target proteins. This analysis is crucial for glycans as a target in drug development, the function of sugars in structure, and the variation of these modifications on protein performance. Moreover, CD BioGlyco also provides Glycoinformatics-assisted Analysis/Prediction Services for clients to study the structure of glycan.
- Services offered by us start with the initial consultation, where we look to learn more about what goals and needs you have for your project. At this stage, we talk about the target molecule, what you expect as an outcome, and if any peculiar problems may arise.
- During data preparation structural information of glycans and proteins are obtained from databases such as Protein Data Bank (PDB) or the clients can optionally provide their datasets. We process this data carefully at our end to make it computationally ready.
- We carry on with docking, a process that consists of using high-performance software solutions like AutoDock Vina, Glide, or ClusPro to foretell the occupation areas and modes. These docking programs are used for modeling the initial contact between glycans and their binding partners.
- A variety of tools, such as Amber and GROMACS help us to perform molecular dynamic simulations. Using these simulations, we can watch glycan-protein complexes move around and see how they change with time while giving us a glimpse into their stability and interaction.
- We also investigate more than simulations. For assessing model performance, we use multiple scoring functions to evaluate and rank binding interactions. This step is crucial for the re-scoring of affinity and subsequent identification of potentially interesting glycan-protein complexes that should be studied in more detail.
- In the end, we report everything that is been analyzed in detail such reports provide visualization of binding interactions, quantitative analysis of the corresponding affinities, and an overall interpretation.
Publication
DOI: 10.3390/molecules28176413
Technology: Molecular docking, Molecular dynamics simulations, Binding free energy calculations, ADMET prediction
Journal: Molecules
IF: 4.2
Published: 2023
Results: This paper investigated the interaction of novel marine sulfated glycosaminoglycans (MSGs) with the receptor binding domain (RBD) of SARS-CoV-2 spiny glycoprotein (SGP). Potential binding sites on the SGP RBD were identified and characterized by molecular docking and molecular dynamics simulations. It was found that MSGs bind stably mainly through electrostatic interactions formed with positively charged amino acid residues, such as Arg and Lys. Among the five initially identified binding sites, site 1 and site 5 were confirmed to be stable binding sites. In addition, glycosylation of the N343 site had little effect on the binding of MSGs. Binding free energy calculations showed that all MSGs exhibited strong binding affinity.ADMET prediction showed that these MSGs had favorable pharmacokinetic properties and low toxicity. This study provides an important theoretical basis for the development of anti-SARS-CoV-2 therapeutic agents.
Fig.1 Five potential binding sites were identified using the blind docking protocol. (Samanta, et al., 2023)
Frequently Asked Questions (FAQs)
- What computational tools are used in the glycoscience docking and interaction analysis service?
The service employs industry-leading software such as AutoDock Vina, Glide, Amber, and GROMACS. These tools enable precise Modeling, docking, and dynamic simulations of glycan-protein interactions.
- Can the service be customized for specific research needs?
Yes, the service is highly customizable. Our team works closely with clients to tailor the methodologies and tools used, ensuring that the service meets the specific objectives and requirements of each research project.
- How do I get started with the service?
To get started, contact CD BioGlyco to discuss your project goals and requirements. Our team provides a customized plan and quote, and once the project scope and timeline are agreed upon, we will commence the modeling and analysis work.
Applications
- Our docking and interaction analysis service can be used to identify glycan-based drug candidates and optimize binding affinities.
- Our docking and interaction analysis service can be used to detail insights into glycan-protein interaction mechanisms.
- Our docking and interaction analysis service can be used to analyze glycosylation effects on protein function and stability.
Advantages
- We employ advanced scoring algorithms to predict binding affinities and evaluate interaction strength with high accuracy.
- We conduct real-time molecular dynamics simulations to observe the behavior of glycan-protein complexes, providing insights into conformational changes and interaction stability.
- We start with an initial consultation to understand project goals and challenges, ensuring that the service aligns closely with research objectives.
At CD BioGlyco, our glycoscience docking and interaction analysis service provides a robust platform for researchers to explore glycan-protein interactions with high precision and reliability, supporting the development of innovative therapeutics and enhancing our understanding of complex biological systems. Please feel free to contact us for more information and we would like to discuss with you for more details.
References
- Samanta, P.; et al. Docking and molecular dynamics simulations clarify binding sites for interactions of novel marine sulfated glycans with SARS-CoV-2 spike glycoprotein. Molecules. 2023, 28(17): 6413.
- Wang, S.; et al. Dissecting the conformation of glycans and their interactions with proteins. Journal of biomedical science. 2020, 27(1): 93.
For research use only. Not intended for any diagnostic use.
Related Services
