Protein-Peptide Docking Service

Welcome to CD ComputaBio, your trusted partner in computational biology and drug discovery. Our specialized protein-peptide docking services offer cutting-edge solutions for understanding and optimizing protein-peptide interactions. With our expertise in AI-driven analysis methods, we provide advanced insights into molecular interactions to accelerate your research and development processes.

What is Protein-Peptide Docking?

Protein-peptide docking is a computational modeling approach that predicts the binding modes and interaction energies between a protein receptor and a peptide ligand. This technique plays a crucial role in understanding biological processes, designing novel therapeutics, and optimizing drug candidates.

Our Services

• Docking System Setup
  At CD ComputaBio, we utilize advanced molecular docking algorithms to predict protein-peptide complexes' binding modes and energetics. Our experts will set up the docking simulations, considering the flexibility of both the protein receptor and peptide ligand to simulate the binding interactions accurately.

Fig 1. CABS-dock modeling with default settings

• Visualization and Analysis
  We provide detailed visualization of the protein-peptide complexes, highlighting key interactions such as hydrogen bonds, hydrophobic contacts, and electrostatic interactions. Our in-depth analysis aids in interpreting the docking results and rationalizing the binding mode.

Fig 2. Visualization of protein-peptide complexes.

• Binding Affinity Prediction
  CD ComputaBio offers reliable binding affinity prediction services to estimate the strength of protein-peptide interactions. Our quantitative analysis provides valuable insights into the binding affinity, helping you prioritize lead candidates for further experimental validation.

Docking Types

Docking Force Fields & Solvation Models Selection

• Docking Force Fields - Empirical force fields, such as CHARMM and AMBER, are commonly used in protein-peptide docking to describe the non-covalent interactions between atoms. These force fields consider parameters such as bond lengths, angles, and dihedrals to calculate the energy of the system.
• Solvation Models - Solvation models play a crucial role in accounting for the solvent effects and electrostatic interactions in protein-peptide docking. We implement solvation models like Generalized Born (GB) or Poisson-Boltzmann (PB) to consider the influence of water molecules on the binding affinity.

With CD ComputaBio's protein-peptide docking service, you can leverage the power of computational biology to explore the intricate interactions between proteins and peptides. Whether you are conducting drug discovery research, protein engineering, or studying signaling pathways, our docking simulations deliver accurate and reliable results to propel your research forward. Trust CD ComputaBio for cutting-edge computational solutions tailored to your specific needs in protein-peptide docking analysis. If you are interested in our services or have any questions, please feel free to contact us.