Protein nanocages, which are hollow, highly symmetric, nanoscale cage-like structures self-assembled from multiple protein subunits, are emerging as powerful target delivery tools. Our expertise in molecular modeling and simulation techniques enables us to provide accurate and efficient simulations of protein nanocages, leading to a deeper understanding of their structure-function relationships and their potential applications in various fields.

Figure 1. Protein nanocages Engineering.( Bhaskar S,et al. 2017)

Services Items

At CD ComputaBio, we offer a full range of services for protein nanocage simulation, tailored to meet your specific research needs. Our team of experienced scientists and computational experts will work closely with you to design and execute simulations that address your scientific questions and achieve your goals. Our services cover the following areas:

• Structure Prediction: We provide state-of-the-art algorithms to predict the 3D structure of protein nanocages, even in the absence of an experimental structure. Our advanced computational approach combines knowledge-based modeling, template-based modeling, and molecular dynamics simulations to generate accurate protein structure models.
• Dynamics simulations: We use molecular dynamics simulations to study the flexibility, stability, and conformational changes of protein nanocages under different conditions. By analyzing the dynamics of these nanocages, we can gain insight into their functional mechanisms and explore the possibility of modifying them to improve their performance.
• Binding studies: Our services include modeling protein-ligand interactions to understand the binding affinity and specificity of protein nanocapsules to small molecules, peptides, or other proteins. These binding studies help to design and optimize protein nanocapsules for drug delivery, enzyme catalysis, or other applications.

Service Highlights

• Customized Approach: We understand that every research project is unique. Therefore, we offer customized simulation approaches to meet your specific research goals and constraints. Our team will work closely with you to design simulations that provide meaningful and accurate results.
• High-quality analysis: Our services include not only simulation but also comprehensive analysis of the resulting data. We provide detailed reports and visualizations to help you interpret the simulation results and gain valuable insights.

Algorithms

Our protein nanocage simulation services are based on a range of cutting-edge algorithms and software tools, including but not limited to

• Molecular dynamics simulation: We use well-established molecular dynamics software packages such as GROMACS and AMBER to simulate the dynamics of protein nanocages.
• Homology Modeling: Our team employs advanced homology modeling algorithms, including MODELLER and SWISS-MODEL, to predict protein structures based on known structural templates.
• Protein-ligand docking: We employ various docking algorithms, such as AutoDock and Vina, to study the binding modes and interaction energies between protein nanocages and ligands.

Why Choose Us?

Our simulations are performed on a high-performance computing cluster, which allows us to handle large-scale computations and obtain accurate and reliable results. Our team consists of scientists with extensive experience in computational biology and drug design. We keep abreast of the latest developments in the field and continuously improve our methods and approaches. Our team looks forward to working with you to realize the full potential of protein nanocages in your research.

Reference

1. Bhaskar S, Lim S. Engineering protein nanocages as carriers for biomedical applications. NPG Asia materials, 2017, 9(4): e371-e371.