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CD ComputaBio leverages advanced molecular modeling and simulation technologies, combined with extensive peptide databases, to provide professional template-based peptide design services. We utilize active peptides with known structures as templates, employing precise computational optimization to efficiently design peptide candidates with significantly enhanced stability and superior bioactivity, widely applicable in fields such as drug development and biotechnology, meeting your personalized needs.
Template-based peptide design rationally constructs novel peptide molecules by utilizing peptides or protein fragments with known structures and functions as templates. These templates can be naturally occurring peptides with specific functions or protein domains known to bind to targets. Through analyzing the sequence, structure, and interaction patterns of the templates, combined with computational simulations (such as molecular docking and molecular dynamics simulations) and data mining, peptide libraries are designed to optimize peptide stability, affinity, or selectivity.
Fig. 1 Schematic template-based design strategy. (TAHMASEBI E, et al., 2020)
| Tools & Servers | Description | References |
| GalaxyPepDock | A web server performs similarity-based docking by finding templates from the database of experimentally determined structures and building models using energy-based optimization that allows for structural flexibility. | Lee et al. (2015) |
| PepComposer | A new pipeline for the computational design of peptides binding to a given protein surface. | Obarska-Kosinska et al. (2016) |
Protein-protein interaction (PPI) interfaces play a crucial role in key functions such as regulating signal transduction, immune responses, and cellular processes between biomolecules. CD ComputaBio utilizes conserved templates from PPI interfaces for peptide design, aiming to provide efficient and precise design solutions for drug development and biomaterials science, thereby accelerating the translation process from experiment to application.
Information Gathering - Conduct research on target types and functional goals based on customer requirements, and determine the design direction (antibacterial, anti-tumor, or receptor modulation).
Template Screening - Select conserved templates from multi-source structural databases (such as PDB and UniProt) based on the characteristics of the protein-protein interaction interfaces of the target.
Template Evaluation - Analyze the structural features of the template, its binding mode with the target, etc., to determine the parts recommended for optimization.
Peptide Design - Perform rational design of peptides based on the template (residue substitution/truncation/cyclization) to generate a candidate peptide library.
Activity Evaluation - Evaluate binding energy and stability through molecular docking and dynamics simulations, and recommend candidate molecules for priority experimental validation.
Template-based Docking
We utilize known complex models to perform template-based docking, aligning the designed peptides with the target to calculate the binding affinity of the peptides.
Molecular Dynamics Simulations
Molecular dynamics simulation is employed by CD ComputaBio to study the dynamic stability of the peptide-target complex and calculate the binding free energy, further validating the docking results.
CD ComputaBio leads innovation in peptide therapeutics by providing template-based peptide design services. Our expert team delivers superior peptide candidates by utilizing technologies such as molecular modeling and artificial intelligence, along with the integration of extensive databases. Contact us today to learn how our specialized services can streamline your peptide drug design and enhance your research outcomes.
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CD ComputaBio offers computation-driven peptide design services to research institutions, pharmaceutical, and biotechnology companies.
