Protein Carbohydrate Docking

Protein Carbohydrate Docking

Services

One-stop

Drug Discovery Services

  • Experienced and qualified scientists functioning as project managers or study director
  • Independent quality unit assuring regulatory compliance
  • Methods validated per ICH GLP/GMP guidelines
  • Rigorous sample tracking and handling procedures to prevent mistakes
  • Controlled laboratory environment to prevent a whole new level of success

Protein Carbohydrate Docking

INQUIRY

Protein-carbohydrate interactions are of vital importance in a variety of biological processes (immunity, metabolism, and immune response) since carbohydrates are usually involved in many essential signaling pathway. Compared to some biophysical approaches in which it's difficult to study these interactions, computational molecular modeling techniques have been widely applied to offer an alternative method for the study of protein-carbohydrate recognition and specificity.

Fig.1 Example of best pose of the protein, the catalytic site, and potential chemical interactions. (Luna-Vital,D.; et al. 2017)Fig.1 Example of best pose of the protein, the catalytic site, and potential chemical interactions. (Luna-Vital,D.; et al. 2017)

Our Procedures And Capabilities

  • Docking

We have designed a docking procedure to explore and identify the orientations and positions of a ligand into a protein cavity.

  • Calculations and clustering

We then perform the calculation and examination of the stability of complexes by using the energy function for carbohydrates to cluster the binding poses and explore the most favorable complex structure.

  • Optimization

We carry out a relative short molecular dynamics simulation run to further evaluate the stability of the complexes and deliver the optimal structure model.

Our Abilities

  1. Our teams apply the docking approach to connect the carbohydrates to the protein binding site using rotations and variations of virtual bonds via dummy atoms.

  2. At BOC Sciences, experiment-derived constraints are available in our docking services to restrict the search space for the sugar as well as the protein molecule.

  3. Our scientists have introduced a molecular mechanical force field to perform conformational analysis of oligosaccharides and this method is also compatible with the subsequent process of protein simulation.

  4. We combine a novel docking algorithm with scoring which is specific to carbohydrate and energy functions to identify accurate ligand poses with high accurate.

Reference

  • Luna-Vital,D.; et al. Anthocyanins from Purple Corn Ameliorated Tumor Necrosis Factor-α-Induced Inflammation and Insulin Resistance in 3T3-L1 Adipocytes via Activation of Insulin Signaling and Enhanced GLUT4 Translocation. Scientific Reports. 2017, 7(1): 3165.

※ It should be noted that our service is only used for research.

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