Structure-based Peptide Design Service

In the first step of structure-based design, computer-aided analysis is used to study targets with or without bound ligands, revealing characteristics such as potential binding sites and other determinants of pharmacological activity, to facilitate subsequent molecular design. Therefore, with the help of computational tools, peptide design ideas can be refined. CD ComputaBio has extensive experience in structure-based peptide design and offers customized solutions for you.

Introduction to Structure-based Peptide Design

In recent decades, various computational tools have been developed to gain a deeper understanding of the structural determinants of interactions. Computer simulations, such as collecting cavity and hotspot data or performing target-peptide docking to study target-peptide complex interfaces, can be used to assist in the rational design of regulatory peptides. Structure-based peptide design uses specific biomolecules (such as proteins, receptors, enzymes, etc.) or biological structures as targets to design peptide molecules that can specifically bind to the targets and exert specific biological functions.

Fig. 1 Structure based peptide design for targeting binding domain. (TIMUCIN A C, 2021)

Our Services

CD ComputaBio utilizes advanced computational technologies and professional biological expertise. Through structural analysis of target sites and the use of molecular simulation, computer-aided design, and other methods, we precisely design peptide sequences with specific functions and activities. This ensures that the designed peptides can better meet the needs of different application scenarios.

Workflow of Structure-based Peptide Design

Binding Site Identification - Identifying the structure of the target protein and its interacting partners, and extracting interface features from the complex.

Rational Peptide Design - Building machine learning models to utilize interface features for constrained peptide design for the target.

Peptide Conformational Search - Narrowing down the peptide sequence search space based on interface features using bioinformatics and other tools.

Binding Affinity Prediction - Predicting and ranking the binding ability of candidate sequences using peptide docking tools or AI tools.

Peptide Candidate Selection - Predicting the kinetic or thermodynamic properties of the peptides to further narrow down the number of peptide sequences selected for experimental determination.

Types of Targets

We can design peptides targeting different targets to serve scientific and clinical purposes. These designed peptides can specifically bind to and modulate receptors, enzymes, and other proteins of interest. By designing their sequences and structures, we can enhance the peptides' binding affinity, stability, and activity. Therefore, this enables them to be used in clinical diagnostics and disease treatment, among other applications.

G Protein-Coupled Receptors

Ion Channels

Receptor Tyrosine Kinases

If you are interested in our structure-based peptide design services or have any questions or requirements, please feel free to contact us. The CD ComputaBio team is dedicated to serving you wholeheartedly and looks forward to collaborating with you to jointly advance the development of the life sciences field.

References:

TIMUCIN, A C. Structure based peptide design, molecular dynamics and MM-PBSA studies for targeting C terminal dimerization of NFAT5 DNA binding domain. Journal of Molecular Graphics and Modelling. 2021, 103: 107804.

For research use only. Not intended for any clinical use.

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