Leveraging state-of-the-art computational technologies and techniques, our expert team can provide accurate, efficient, and high-quality docking solutions tailored to your unique research needs. CD ComputaBio offers a comprehensive rigid docking service designed to streamline the molecular docking process for pharmaceutical and biotechnology companies.
Introduction to Rigid Docking
Rigid Docking focuses on predicting how small molecules, specifically ligand candidates, bind to their target macromolecules, typically proteins. In the rigid docking approach, the protein is considered to be a rigid structure, simplifying the calculations and reducing the computational resources required. This method is particularly effective in the initial phases of drug design, where speed and efficiency are paramount.
Figure 1. Schematics for construction of rigid docking. ( Luo Q ,et al. 2024)
Advantages of Rigid Docking
High Computational Efficiency
During calculation, rigid docking treats molecules as rigid structures, reducing complex conformational search steps. This significantly simplifies the calculation process.
Easily Interpretable Model
By not considering the complex changes brought about by molecular flexibility, the model established by rigid docking is relatively stable. Researchers can analyze the binding modes between molecules more intuitively and clearly.
Great Value for Fundamental Research
When initially exploring the principles of intermolecular interactions, rigid docking can provide fundamental and effective information, contributing to the exploration of the basic laws of biomolecular interactions.
Our Service
Leveraging advanced technological platforms, our professional team focuses on treating molecules as rigid entities during the docking process. Our primary objective is to assist scientific researchers in unlocking the mysteries of protein-small molecule interactions in a concise yet highly efficient manner.
Preprocessing of Rigid Docking
For protein structures, we will carry out a series of preprocessing steps. For systems without protein crystal structures, we offer the following services, including:
For small molecules, This can be retrieved from chemical databases such as PubChem and ChemSpider, or it can come from in-house experimental data. We can convert the ligand structure into a format that is compatible with the docking software.
Basic Rigid Docking Screening
We perform rigid docking of the entire ligand library using a standard set of docking parameters optimized for high-throughput screening. The output includes a ranked list of ligands based on their predicted binding energies, along with visualizations of the top binding modes.
Complex Analysis and Interaction Studies
Although it is mainly rigid docking, we can reveal the binding interaction sites and highlight the key residues involved in ligand binding. We calculate the interaction energy to assess the stability of ligand-receptor complexes and present the results in a user-friendly format. Our analysis services include:
Applications of Rigid Docking
Rigid docking has extensive applications across a wide variety of molecular arenas. For researchers eager to dissect the fundamental aspects of molecular interactions, this docking is an extremely valuable resource. The rigid docking method can be applied to the analysis of the following molecular systems, including:
Service Features
High-Throughput Screening
Rigid docking enables rapid screening of large compound libraries. It can quickly assess the binding potential of numerous ligands to a receptor.
Commitment to Client Success
We are dedicated to ensuring you have access to the resources and guidance necessary throughout your research project.
Expertise and Experience
Our expertise in molecular docking allows us to provide high-quality results that can assist in your drug discovery efforts.
Get Started Today!
CD ComputaBio's rigid docking service stands out as a premier solution for researchers seeking to enhance their drug discovery efforts. By choosing our rigid docking service, you gain access to a dedicated team committed to helping you navigate the complexities of molecular docking. Contact us today to learn more about how our service assist you in achieving your research and development goals.
Reference:
- Luo Q, Wang S, Li H Y, et al. Benchmarking reverse docking through AlphaFold2 human proteome. Protein Science, 2024, 33(10): e5167.
* For Research Use Only.
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