Protein Interaction Based Peptide Design

An interaction between two proteins usually consists of a large interface without a well-characterized binding pocket. Peptides could be good starting points for new leads in the rational design of inhibitory drugs by mimicking part of the interacting surface of one of the proteins. This feature is particularly suitable for immune checkpoints drug development. As an industry-leading CRO company, Creative Biolabs has developed an advanced technology platform with Ph.D. level experts specialized in peptide design and bioinformatics. With professional expertise and rich experience, we have accomplished hundreds of customers' projects. The strong foundations and excellent reputation are the best guarantees of our services.

Protein Interaction Based Peptide Design


A prominent place to start looking for drug candidates is by examining the complementary surfaces of the binding partners at the interaction sites. The specificity with which a drug selects a particular protein depends on the detailed nature of the protein-protein interaction (PPI) site in terms of the 3D placement and identity of protein surface amino acid residues. Peptides are the ideal starting place from which to derive inhibitors of PPIs. This leads to a straightforward concept for PPI inhibitors. PPIs play a crucial role in many cellular processes and pathways, especially for immune checkpoint pathways. Thus, the development of small molecules that affect PPIs has become an intensive research field in structural bioinformatics and computer-aided drug design.

With professional technical scientists and abundant experience in immune checkpoint drug development, the task at Creative Biolabs is to discover small molecules that will block specific immune checkpoint pathways without harming the function of other proteins. Some of those desired inhibitors include small-molecule inhibitors and especially short peptide inhibitors. Due to the diversity of the peptides and PPIs, Creative Biolabs could perform the most effective method for protein interaction-based peptide design (bioinformatic approach with the aid of computer calculation) to meet your specific requirements.

Two Examples for Peptide Interaction Based Peptide Design

Fig. 1 Protein interaction based peptide design. (
  • PepCrawler
  • PepCrawler is a tool for predicting protein-peptide complexes at high resolution and the derivation of binding peptides out of protein-protein complexes interface. This method exploits the RRT (Rapidly exploring Random Tree) robotics motivated methodology. The output is a protein peptide complex depicting the final predicted peptide conformation (the one with the best computational energy score). It also outputs a funnel score (the slope of the Energy/RMSD plot), a measurement of the peptide likelihood to achieve the predicted conformation.

  • PinaColada
  • PinaColada is a method for computational screening of peptides to find novel inhibitors for PPIs. It uses the ant colony optimization (ACO) method to explore the peptide sequence space. ACO has the nature of combining reasonable partial solutions to better global solutions due to its inherent balance between exploration and exploitation.

Focusing on immune checkpoint drug development for more than ten years, Creative Biolabs is professional in protein interaction-based peptide design. Our technology platform covers various advanced methods and techniques for peptide design, and our experts will help you find the most suitable one for your research. If you are interested in protein interaction-based peptide design services or any other services on our website, please feel free to contact us for more information.

All listed customized services & products are for research use only, not intended for pharmaceutical, diagnostic, therapeutic, or any in vivo human use.

  • Protein Structure Based Peptide Design