Creative BioMart provides protein-peptide docking service to predict the structure of protein-peptide complexes based on protein structures and peptide sequences, offering a broad prospect for peptides as promising drug candidates. 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.

Interactions between proteins are fundamental components of many biological processes, 40% of which are mediated by short peptides. Chemical similarities to proteins have recently drawn widespread attention to peptides as promising drug candidates. The design of popular peptide-derived therapies relies heavily on underlying protein-peptide interactions. Determining the structure of protein-peptide complexes is critical for understanding molecular mechanisms and modulating protein-peptide interactions for therapeutic purposes. Only a limited number of protein-peptide complex structures can be determined experimentally. Therefore, computational models like molecular docking play an important role in determining the structure of protein-peptide complexes.

Fig 1. Typical pipelines for protein–peptide molecular docking. (Ciemny M, et al., 2018)

Compared with protein-ligand docking and protein-protein docking, protein-peptide docking faces two challenges. First, unlike protein-ligand docking where the binding site is generally known, information on the binding site of the peptide is not available in many cases. Second, compared to small compounds and proteins, peptides are more flexible and do not have a stable conformation until they bind to receptors. Creative BioMart utilizes various state-of-the-art algorithms for protein-peptide docking to perform global searches around entire proteins to predict protein-peptide binding modes, including different degrees of information about the peptide binding site and/or conformation.

Protein-peptide docking is increasingly incorporated into drug discovery and design processes, and our scientists predict the structure of protein-peptide complexes starting from random conformations and positions of peptides based on the following protein-peptide docking method. We can provide professional solutions for modeling large-scale conformational changes after combining, scoring prediction models, and optimally incorporating various types of experimental data and theoretical predictions into comprehensive modeling processes.

• Template-based docking.
• local docking.
• Global docking.

Features of Protein-Peptide Docking

• Quantum mechanical calculations within the docking point to fine-tune the docking pose.
• Predictions only take seconds and serve as quick estimates for narrowing down the search space.
• Accepting structure or sequence as protein input.
• Automatic integration of available peptide binding information from the Protein Data Bank (PDB).
• Nucleic acid-peptide docking.
• The docking process is fully automatic.
• The results are interactively presented to the user through a web page.
• No prior knowledge of binding site or peptide conformation is required.
• Peptide conformation allows complete flexibility.

Reference

1. Ciemny M, Kurcinski M, et al.. (2018) Protein-peptide docking: opportunities and challenges. Drug Discov Today. 23 (8): 1530 - 1537.

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