Glycoinformatics-assisted Custom Modeling Service
Mastering Glycan Structures with Computational Precision and Comprehensive Data Integration
CD BioGlyco offers glycoinformatics-assisted custom modeling as a made-to-order service. We use advanced computational tools to Model and Analyze Glycan Structures accurately. In addition to modeling tools, we also integrate protein databases with the glycoinformatics service. Our service also integrates databases such as the Protein Data Bank (PDB) for extracting glycoproteins and protein-carbohydrate complex data, and automated molecular geometry processing tools such as GlyTorsion and GlyVicinity for detailed structural analysis. The comprehensive data calls allow us to perform comprehensive glycan modeling, including structure prediction, conformational analysis, and docking simulations.
Fig.1 Networking and integration of glycoinformatics projects and associated services. (Scherbinina & Toukach, 2020)
Our glycoinformatics-assisted custom modeling uses advanced tools and databases to predict, model, and analyze glycan structures and their interactions. The key tools include GLYCAM-Web for glycan structure prediction and glycosylated protein modeling, CHARMM-GUI for 3D glycan modeling, and Glycosylator for rapid glycan and glycoprotein modeling. RosettaCarbohydrate offers capabilities for saccharide and glycoconjugate modeling, including loop modeling and glyco-ligand docking. For structure building and model preparation, tools like doGlycans, POLYS, CarbBuilder, and GAG-builder are used. Docking tools such as BALLDock/SLICK, HADDOCK, and Vina-Carb facilitate protein-carbohydrate interaction studies. Data analysis tools like CAT, BFMP, MD2NOE, GS-align, GlyTorsion, and GlyVicinity are employed for conformational analysis and validation. This comprehensive approach allows for detailed study and simulation of glycan behavior, enhancing the understanding of glycosylation processes and aiding in the development of carbohydrate-based therapeutics.
Publication
DOI: 10.5772/56376
Technology: Molecular docking
Journal: Protein engineering-technology and application
Published: 2013
Results: Molecular docking simulates a ligand and protein in free solution to model the natural binding process using an approach of mimicking their interaction downhill lowest energy pathway. This takes into consideration a wide range of forces: hydrophobic interactions, van der Waals forces, hydrogen bonding and electrostatic battles. Docking may also be rigid (both molecules are inflexible), or flexible in the ligand and, possibly on a trial basis of flexibility accorded to regions of protein). The docking protocol consists of a search algorithm to sample binding modes and a scoring function to estimate the relative free energy. Molecular dynamics and Monte Carlo methods are common but scoring functions that evaluate binding modes, affinities or predicting druggability using force-field or empirical ways constitute an important part of drug discovery. Flexible docking Flexible protein-docking models soft dock structures, e. g., free-energy methods or structural ensemble approaches.
Fig.2 Methods used for protein-ligand docking. (Hernández-Santoyo, et al., 2013)
Applications
- Our custom modeling service can be used to predict binding affinities and modes, aiding in the optimization of drug candidates.
- Our custom modeling service can be used to identify and map glycan epitopes to enhance vaccine efficacy.
- Our custom modeling service can be used to model the glycosylation of proteins to understand their role in cellular processes.
Advantages
- We use sophisticated tools like GLYCAM-Web, CHARMM-GUI, and RosettaCarbohydrate for accurate glycan modeling.
- We provide customized modeling services to meet specific research needs and objectives.
- We leverage extensive databases like GlyTouCan and PDB for accurate data integration.
- We use predictive tools to forecast glycan interactions and binding affinities, aiding in drug and vaccine development.
Frequently Asked Questions (FAQs)
- What is the glycoinformatics-assisted custom modeling service?
Our custom modeling service is a specialized service that uses advanced computational tools and glycoinformatics to model, predict, and analyze the structures and interactions of carbohydrate molecules, such as glycans, glycoproteins, and glycan-ligand complexes.
- Can the service model both rigid and flexible molecules?
Yes, the service can handle both rigid and flexible molecules. Rigid docking models molecules as inflexible entities, while flexible docking accounts for the conformational changes of ligands and, potentially, protein receptors. This comprehensive approach ensures an accurate representation of molecular interactions and binding modes.
At CD BioGlyco, our custom modeling service provides extensive applications in drug discovery, vaccine design, and biological research, coupled with significant advantages in precision, efficiency, customization, and predictive capabilities. Please feel free to contact us for information if you are interested in our Modeling Service!
References
- Scherbinina, S.I.; Toukach P.V. Three-dimensional structures of carbohydrates and where to find them. International journal of molecular sciences. 2020, 21(20): 7702.
- Hernández-Santoyo, A.; et al. Protein-protein and protein-ligand docking. Protein engineering-technology and application. 2013, 63-81.
For research use only. Not intended for any diagnostic use.
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