Protein Peptide Docking

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Protein Peptide Docking

INQUIRY

Peptides have been widely used in the docking progress, for they cover a much larger surface area when interacting with the 'hot-spots' on the binding surface of a protein target. Peptides can therefore interact with their targets with high specificity and biologically relevant affinity. These kind of interactions play important roles in living organisms and they are concluded in a variety of signaling pathways including cellular localization, immune response or protein expression and degradation. Scientists use the crucial information of such interactions to investigate various interactions associated diseases.

Fig.1 Molecular visualizations of the protein-peptide docking. (Kurcinski, M.; et al. 2020)Fig.1 Molecular visualizations of the protein-peptide docking. (Kurcinski, M.; et al. 2020)

Docking Process And Our Services

  • Docking

We perform a search to give reliable predictions of the binding site at the protein receptor surface.

  • Scoring

We apply the obtained predicted data on binding site to constrain the docking to local regions of the protein surface.

  • Ranking

The best-scored structures are clustered and ranked, and the largest clusters with low-energy conformations are chosen for high-quality structural refinement.

Our Capabilities

  1. We can provide convincing identification of hot-spot residues and accurate prediction of binding affinity.

  2. We also observe and search for structural units of peptides with their binding pocket within not only interfaces but also monomers.

  3. In the docking stages, we provide the services of simulating peptide folding process.

  4. Our groups can simulate the significant conformational changes of protein-peptides complex interactions, and the peptide conformation allows to be fully flexible.

  5. We are capable of carrying out high-resolution structural refinement and characterization before delivering the final structures.

  6. At BOC Sciences, modification of amino acids in both proteins and peptides are available.

  7. Our docking approach can also be applied to study the peptide-protein association, and to design the new peptide binder for multiple purposes.

Reference

  • Kurcinski, M.; et al. Flexible docking of peptides to proteins using CABS-dock. Protein Science. 2020, 29(1): 211-222.

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

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