Creative BioMart provides protein-carbohydrate docking service to predict these protein-carbohydrate interactions by combining genetic conformation search algorithms with carbohydrate-specific empirical free energy functions. With years of protein engineering research experience, we can provide you with the best quality and most professional services. If you are interested in our services, please do not hesitate to contact us for more information.

Protein-carbohydrate interactions play critical roles in many important biological processes, affecting cell growth, differentiation, and aggregation. Attempts to apply sugars and/or lectins in the pharmaceutical field have been successful, such as coating particles with sugars to enhance cancer treatment. These interactions are difficult to study by X-ray crystallography because sugar moieties often have heterogeneous chemical structures and conformations. Therefore, predicting the binding mode (pose) and binding affinity of protein-carbohydrate complexes is an important issue in computer-aided drug design, and understanding protein-carbohydrate interactions is helpful for drug research and drug design.

Fig 1. The interplay between experimental and theoretical methods required to decipher the structural basis of protein–carbohydrate interactions. (Perez S, et al., 2014)

Docking of carbohydrate ligands is difficult due to the shallow carbohydrate binding site and the very flexible carbohydrate ligands. Creative BioMart specifically designs carbohydrates or carbohydrate-like dockings to handle proteins. Our designed docking procedure combines an evolutionary docking algorithm for flexible ligands and flexible receptor side chains with carbohydrate-specific scoring and energy functions. Furthermore, it allows the system to explore the orientation and location of carbohydrate ligands into protein cavities and to assess protein-carbohydrate complex structures.

The successful computational models of interactions we designed are well received by customers worldwide and are widely used in the virtual screening and lead optimization of carbohydrates. For both applications, we employ the method of ligand docking. Two key parts are relied upon: a search algorithm for sampling the conformational space and an energy or scoring function for evaluating binding energies. To do this, we employ a number of algorithms and scoring functions.

Features of Protein-Carbohydrate Docking

• All data is freely available through a user-friendly web interface and application programming interface.
• Graph-based structural features.
• Supports monosaccharide, disaccharide and oligosaccharide docking.
• Specific to assessing protein-carbohydrate interactions.
• Ability to in silico glycosylate proteins and build 3D models of glycan attachment.

References

1. Perez S, Tvaroška I. (2014) Carbohydrate–protein interactions: Molecular modeling insights[J]. Advances in carbohydrate chemistry and biochemistry. 71: 9-136.
2. Kerzmann A. (2006) SLICK-New Methods for Protein-Carbohydrate Docking[D]. Universität Tübingen.

• Antibody-Antigen Docking
• Protein-Ligand Docking
• Protein-Lipid Docking
• Protein-Nucleic Acid Docking
• Protein-Peptide Docking
• Protein-Protein Docking